Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection.
Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection.
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DOI：
10.1186/s12866-014-0308-1
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发表时间：
2014-12-10
期刊：
影响因子：
4.2
通讯作者：
Dixelius C
中科院分区：
文献类型：
--
作者：
Åsman AK;Vetukuri RR;Jahan SN;Fogelqvist J;Corcoran P;Avrova AO;Whisson SC;Dixelius C
卵菌Phytophthora infestans具有活跃的RNA沉默途径，这可能使这种植物病原体能够控制其240 Mb基因组中存在的大量转座因子。小RNA（sRNA），RNA沉默的中心分子，已知也在这种生物体中发挥关键作用，特别是在调节感染其马铃薯宿主所需的关键效应基因中。为了鉴定卵菌中的其他类别的sRNA，我们将深度测序读数映射到转移RNA（tRNA），从而揭示了19-40 nt tRNA衍生的RNA片段（tRF）的存在。北方印迹分析鉴定了对应于半tRNA分子的丰富的tRF。一些tRFs在感染过程中差异性地积累，如通过检查从致病疫霉-马铃薯相互作用文库测序的sRNA所看到的。通过使用发夹RNA介导的RNAi来沉默编码致病疫霉Argonaute（PiAgo）和Dicer（PiDcl）内切核糖核酸酶的基因，研究了tRF生物发生与经典RNA沉默途径之间的假定联系。通过sRNA测序，我们发现，tRF积累是PiDcl 1独立的，而北方杂交检测到特定的tRNA衍生的物种在PiAgo 1敲低线的水平降低。我们的研究结果扩展了卵菌中sRNA的多样性，包括来自非蛋白编码RNA转录本的片段，并确定了马铃薯感染致病疫霉期间水平升高的tRFs。本文的在线版本（doi：10.1186/s12866-014-0308-1）包含补充材料，可供授权用户使用。
The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19–40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. The online version of this article (doi:10.1186/s12866-014-0308-1) contains supplementary material, which is available to authorized users.
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影响因子：
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作者：
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