School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
Cellular and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, USA.
BMC Genomics. 2021 Jan 9;22(1):42. doi: 10.1186/s12864-020-07322-2.
RNA interference (RNAi) regulates gene expression in most multicellular organisms through binding of small RNA effectors to target transcripts. Exploiting this process is a popular strategy for genetic manipulation and has applications that includes arthropod pest control. RNAi technologies are dependent on delivery method with the most convenient likely being feeding, which is effective in some animals while others are insensitive. The two-spotted spider mite, Tetranychus urticae, is prime candidate for developing RNAi approaches due to frequent occurrence of conventional pesticide resistance. Using a sequencing-based approach, the fate of ingested RNAs was explored to identify features and conditions that affect small RNA biogenesis from external sources to better inform RNAi design.
Biochemical and sequencing approaches in conjunction with extensive computational assessment were used to evaluate metabolism of ingested RNAs in T. urticae. This chelicerae arthropod shows only modest response to oral RNAi and has biogenesis pathways distinct from model organisms. Processing of synthetic and plant host RNAs ingested during feeding were evaluated to identify active substrates for spider mite RNAi pathways. Through cataloging characteristics of biochemically purified RNA from these sources, trans-acting small RNAs could be distinguished from degradation fragments and their origins documented.
Using a strategy that delineates small RNA processing, we found many transcripts have the potential to enter spider mite RNAi pathways, however, trans-acting RNAs appear very unstable and rare. This suggests potential RNAi pathway substrates from ingested materials are mostly degraded and infrequently converted into regulators of gene expression. Spider mites infest a variety of plants, and it would be maladaptive to generate diverse gene regulators from dietary RNAs. This study provides a framework for assessing RNAi technology in organisms where genetic and biochemical tools are absent and benefit rationale design of RNAi triggers for T.urticae.
RNA 干扰（RNAi）通过小 RNA 效应物与靶转录本结合，调节大多数多细胞生物中的基因表达。利用这一过程是遗传操作的一种流行策略，其应用包括节肢动物害虫防治。RNAi 技术依赖于递送方法，最方便的方法可能是喂食，这在一些动物中有效，而在其他动物中则无效。二斑叶螨（Tetranychus urticae）是开发 RNAi 方法的首选候选者，因为其经常出现常规农药抗性。本研究采用基于测序的方法，探索了摄入 RNA 的命运，以确定影响外源小 RNA 生物发生的特征和条件，从而更好地为 RNAi 设计提供信息。
本研究结合生物化学和测序方法以及广泛的计算评估，评估了 T. urticae 中摄入 RNA 的代谢。这种螯肢类节肢动物对口服 RNAi 的反应仅适度，其生物发生途径与模式生物不同。评估了在喂食过程中摄入的合成和植物宿主 RNA 的加工，以鉴定蜘蛛螨 RNAi 途径的活性底物。通过对这些来源的生化纯化 RNA 的特征进行编目，可以区分转座小 RNA 与降解片段，并记录其来源。
本研究采用一种区分小 RNA 加工的策略，发现许多转录本有可能进入蜘蛛螨 RNAi 途径，但转座 RNA 似乎非常不稳定且罕见。这表明，从摄入的物质中产生的潜在 RNAi 途径底物大多被降解，很少转化为基因表达的调节剂。叶螨侵害各种植物，从饮食 RNA 生成多样化的基因调节剂是不利的。本研究为评估缺乏遗传和生化工具的生物体中的 RNAi 技术提供了一个框架，并为 T.urticae 的 RNAi 触发的合理设计提供了益处。
