RNAi effector diversity in nematodes.
RNAi effector diversity in nematodes.
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DOI：
10.1371/journal.pntd.0001176
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发表时间：
2011-06
影响因子：
3.8
通讯作者：
Maule AG
中科院分区：
文献类型：
--
作者：
Dalzell JJ;McVeigh P;Warnock ND;Mitreva M;Bird DM;Abad P;Fleming CC;Day TA;Mousley A;Marks NJ;Maule AG
虽然RNA干扰（RNAi）已被部署，以促进基因功能的研究在不同的蠕虫，寄生线虫似乎易受感染。为了测试这是否是由于RNAi效应互补物的物种间差异，我们对13种线虫物种中77种秀丽隐杆线虫RNAi途径蛋白的直系同源物进行了初步序列相似性调查，其中基因组或转录组数据集可用，所有输出都经过结构域验证。我们的数据集涵盖了犬钩虫和齿食道口线虫的转录组，旋毛虫、猪蛔虫、马来丝虫、捻转血矛线虫、北方根结线虫、南方根结线虫和太平洋孤线虫的基因组，以及小杆线虫C. brenneri，C.布里格塞角japonica和C. remanei，并透露：（i）大多数C. elegans中负责摄取和传播外源施加的双链（ds）RNA的蛋白质在寄生物种（包括RNAi感受态植物线虫）中不存在;与在通过外源dsRNA诱导RNAi期间招募的那些不同，线虫是广泛保守的;（iii）次级Argonautes（SAGREN）是保守性差的，并且在任何寄生虫中均未鉴定出核AGO NRDE-3;（iv）所有五种小杆线虫属（Caelorhabditis spp.）相对于寄生线虫，具有扩展的RNAi效应子库，与线虫寄生虫中基因丢失的倾向一致;（V）尽管线虫物种间RNAi效应子互补物的数量差异，但全部显示功能蛋白质组的定性相似覆盖。总之，我们无法鉴定与寄生线虫易感性降低相关的RNAi效应子缺陷。事实上，RNAi抗性和感受态线虫寄生虫的RNAi效应子互补物的相似性支持了这种研究遗传工具在线虫中的广泛适用性。许多生物体通过RNA干扰（RNAi）途径调节基因表达，首先在线虫秀丽隐杆线虫中表征。这种途径可以通过实验使用双链（ds）RNA来触发选定的基因靶点，从而使研究人员能够“沉默”单个基因，从而研究它们的功能。人们希望这项技术将有助于对人类造成相当大的健康和经济负担的重要寄生线虫的基因沉默。不幸的是，已经观察到物种之间RNAi易感性的差异。在这里，我们调查的可能性，参与RNAi途径的效应蛋白的互补的差异是负责这些差异的易感性。我们的数据显示，RNAi途径的大多数方面在寄生线虫中都有很好的代表性，尽管与C.优雅相反，负责摄取和传播dsRNA的蛋白质在寄生线虫中没有很好的代表性。然而，这些差异的重要性被我们的观察所削弱，即所有寄生虫中的蛋白质互补物在性质上是相似的，而不管RNAi敏感性如何。显然，寄生线虫RNAi途径的差异不能解释实验RNAi敏感性的变化。
While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes. Many organisms regulate gene expression through an RNA interference (RNAi) pathway, first characterized in the nematode Caenorhabditis elegans. This pathway can be triggered experimentally using double-stranded (ds)RNA to selected gene targets, thereby allowing researchers to ‘silence’ individual genes and so investigate their function. It is hoped that this technology will facilitate gene silencing in important parasitic nematodes that impose a considerable health and economic burden on mankind. Unfortunately, differences in RNAi susceptibility have been observed between species. Here we investigated the possibility that differences in the complement of effector proteins involved in the RNAi pathway are responsible for these differences in susceptibility. Our data revealed that most facets of the RNAi pathway are well represented across parasitic nematodes, although there were fewer pathway proteins in other nematodes compared to C. elegans. In contrast, the proteins responsible for uptake and spread of dsRNA are not well represented in parasitic nematodes. However, the importance of these differences is undermined by our observation that the protein complements in all the parasites were qualitatively similar, regardless of RNAi-susceptibility. Clearly, differences in the RNAi pathway of parasitic nematodes do not explain the variations in susceptibility to experimental RNAi.
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DOI：
10.1073/pnas.0906378106
发表时间：
2009-11-03
影响因子：
11.1
作者：
Han, Ting;Manoharan, Arun Prasad;Kim, John K.
通讯作者：
Kim, John K.
影响因子：
56.9
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影响因子：
48
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通讯作者：
Chalfie, Martin
DOI：
10.1073/pnas.0604698103
发表时间：
2006-09-26
影响因子：
11.1
作者：
Huang, Guozhong;Allen, Rex;Hussey, Richard S.
通讯作者：
Hussey, Richard S.
影响因子：
4.5
作者：
Chan, Shih-Peng;Ramaswamy, Gopalakrishna;Slack, Frank J.
通讯作者：
Slack, Frank J.