ABSTRACT

RNA interference (RNAi)-mediated gene silencing can be used to control specific insect pest populations. Unfortunately, the variable efficiency in the knockdown levels of target genes has narrowed the applicability of this technology to a few species. Here, we examine the current state of knowledge regarding the miRNA (micro RNA) and siRNA (small interfering RNA) pathways in insects and investigate the structural variability at key protein domains of the RNAi machinery. Our goal was to correlate domain variability with mechanisms affecting the gene silencing efficiency. To this end, the protein domains of 168 insect species, encompassing the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera, were analysed using our pipeline, which takes advantage of meticulous structure-based sequence alignments. We used phylogenetic inference and the evolutionary rate coefficient (K) to outline the variability across domain regions and surfaces. Our results show that four domains, namely dsrm, Helicase, PAZ and Ribonuclease III, are the main contributors of protein variability in the RNAi machinery across different insect orders. We discuss the potential roles of these domains in regulating RNAi-mediated gene silencing and the role of loop regions in fine-tuning RNAi efficiency. Additionally, we identified several order-specific singularities which indicate that lepidopterans have evolved differently from other insect orders, possibly due to constant coevolution with plants and viruses. In conclusion, our results highlight several variability hotspots that deserve further investigation in order to improve the application of RNAi technology in the control of insect pests.

摘要

RNA 干扰 (RNAi) 介导的基因沉默可用于控制特定的害虫种群。不幸的是，靶基因敲低水平的可变效率已将这项技术的适用范围缩小到少数物种。在这里，我们检查了有关昆虫中 miRNA（微小 RNA）和 siRNA（小干扰 RNA）途径的知识现状，并研究了 RNAi 机器关键蛋白质结构域的结构变异性。我们的目标是将域变异性与影响基因沉默效率的机制相关联。为此，使用我们的管道分析了 168 种昆虫的蛋白质结构域，包括鞘翅目、双翅目、半翅目、膜翅目和鳞翅目，该管道利用了基于结构的精确序列比对。K ) 概述跨域区域和表面的可变性。我们的研究结果表明，四个域，即 dsrm、解旋酶、PAZ 和核糖核酸酶 III，是不同昆虫目 RNAi 机制中蛋白质变异的主要贡献者。我们讨论了这些结构域在调节 RNAi 介导的基因沉默中的潜在作用以及环区域在微调 RNAi 效率中的作用。此外，我们确定了几个特定于特定目的的奇点，这些奇点表明鳞翅目动物的进化与其他昆虫目不同，这可能是由于与植物和病毒的不断共同进化。总之，我们的研究结果突出了几个值得进一步研究的变异热点，以改进 RNAi 技术在害虫控制中的应用。