Institute of Plant Protection, Agricultural Research Organization, the Volcani Center, P.O.B 15159, 7505101, Rishon leZion, Israel.
BMC Genomics. 2020 Nov 12;21(1):791. doi: 10.1186/s12864-020-07162-0.
RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari.
Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group.
Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.
RNA 干扰（RNAi）是一种高度保守的、存在于真核生物中的序列特异性基因沉默机制。目前已知有三种 RNAi 途径，即 micro-RNA（miRNA）、piwi-interacting RNA（piRNA）和短干扰 RNA（siRNA）。然而，关于节肢动物中这些途径涉及的蛋白质知之甚少。此外，通过 siRNA 途径在功能基因组学和管理中进行基因敲低的成功率各不相同。我们假设，原因可能在于节肢动物中 siRNA 机制的组成和功效的可变性。
比较基因组分析和结构域注释都表明，所有分析的物种都具有介导通过三种 RNAi 途径切割靶向基因的核心蛋白的假定同源物。我们在所有物种中都鉴定出了假定的秀丽隐杆线虫 RNA 依赖性 RNA 聚合酶（RdRP）蛋白的同源物，尽管没有发现与 siRNA 扩增机制中该蛋白协同作用的二级 Argonaute 同源物，但这表明节肢动物中存在的 siRNA 扩增机制可能与秀丽隐杆线虫中描述的机制不同。此外，这些物种的基因组不编码秀丽隐杆线虫系统性 RNAi 缺陷-1（Sid-1）蛋白的同源物，该蛋白介导整个处理生物体中 mRNA 靶标的沉默，这表明在一些节肢动物物种中报道的系统性 RNAi 现象可能通过不同的机制发生。然而，在节肢动物的基因组中发现了假定的 RNAi 扩散缺陷-3（Rsd-3）蛋白和吞噬受体 Eater 和 SR-CI 的同源物，这些蛋白在秀丽隐杆线虫和黑腹果蝇中介导 dsRNA 的细胞内更新。这一结果表明，节肢动物中的细胞 dsRNA 摄取是内吞作用依赖性的。对所研究物种中核心 RNAi 途径蛋白的详细系统发育分析表明，它们的进化与该组提出的单系进化是一致的。
我们的分析表明，所有三种途径在节肢动物中都具有潜在的活性。然而，仍需要进行大量的实验工作来证实这些途径背后的机制，特别是那些控制节肢动物中系统性/亲代 RNAi 和 siRNA 扩增的机制。揭示这些机制将有助于为有害物种开发新的和特定的管理工具，并丰富有益物种。
