Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis.
Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis.
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DOI：
10.1371/journal.pone.0007539
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发表时间：
2009-10-21
期刊：
影响因子：
3.7
通讯作者：
Flores R
中科院分区：
文献类型：
--
作者：
Di Serio F;Gisel A;Navarro B;Delgado S;Martínez de Alba AE;Donvito G;Flores R
Northern印迹杂交和低规模测序已经揭示，被类病毒（非蛋白质编码RNA复制子）感染的植物积累21-24 nt类病毒衍生的小RNA（vd-sRNA），类似于小干扰RNA，RNA沉默的标志。这些结果强烈支持类病毒是其宿主RNA沉默机制的激发子和靶标。然而，低规模测序检索部分数据集，并可能导致有偏见的解释。为了克服这种限制，我们已经通过深度测序（Solexa-Illumina）和计算方法检查了在GF-305桃幼苗中积累的vd-sRNA，所述桃幼苗被桃潜伏花叶类病毒（PLMVd）的两种分子变体感染，所述两种分子变体引发桃花斑病（白化病）和桃花叶。我们的研究结果表明，在这两个样品中，多个PLMVd-sRNA，与普遍的21-nt（+）和（−）RNA呈现出其5′核苷酸的偏倚分布，并采用热点概况沿着基因组（+）和（−）RNA。Dicer样4和2（分别为DCL 4和DCL 2）在抗病毒防御中分级作用，可能也介导21-和22-nt PLMVd-sRNA的发生。更具体地，因为PLMVd在质体中复制，其中RNA沉默尚未被报道，所以DCL 4和DCL 2应该在它们的细胞质移动期间切割PLMVd基因组RNA或由细胞质RNA依赖性RNA聚合酶（RDR）（如RDR 6）产生的PLMVd-dsRNA，其与DCL 4加工协同作用。此外，考虑到来源于含有桃印花病致病性决定子的12-14-nt插入的vd-sRNA代表性不足，症状不太可能是由来自该决定子的vd-sRNA偶然靶向宿主mRNA导致的，该决定子引导RNA沉默机制。
Northern-blot hybridization and low-scale sequencing have revealed that plants infected by viroids, non-protein-coding RNA replicons, accumulate 21–24 nt viroid-derived small RNAs (vd-sRNAs) similar to the small interfering RNAs, the hallmarks of RNA silencing. These results strongly support that viroids are elicitors and targets of the RNA silencing machinery of their hosts. Low-scale sequencing, however, retrieves partial datasets and may lead to biased interpretations. To overcome this restraint we have examined by deep sequencing (Solexa-Illumina) and computational approaches the vd-sRNAs accumulating in GF-305 peach seedlings infected by two molecular variants of Peach latent mosaic viroid (PLMVd) inciting peach calico (albinism) and peach mosaic. Our results show in both samples multiple PLMVd-sRNAs, with prevalent 21-nt (+) and (−) RNAs presenting a biased distribution of their 5′ nucleotide, and adopting a hotspot profile along the genomic (+) and (−) RNAs. Dicer-like 4 and 2 (DCL4 and DCL2, respectively), which act hierarchically in antiviral defense, likely also mediate the genesis of the 21- and 22-nt PLMVd-sRNAs. More specifically, because PLMVd replicates in plastids wherein RNA silencing has not been reported, DCL4 and DCL2 should dice the PLMVd genomic RNAs during their cytoplasmic movement or the PLMVd-dsRNAs generated by a cytoplasmic RNA-dependent RNA polymerase (RDR), like RDR6, acting in concert with DCL4 processing. Furthermore, given that vd-sRNAs derived from the 12–14-nt insertion containing the pathogenicity determinant of peach calico are underrepresented, it is unlikely that symptoms may result from the accidental targeting of host mRNAs by vd-sRNAs from this determinant guiding the RNA silencing machinery.
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影响因子：
7.2
作者：
Gomez, G.;Pallas, V.
通讯作者：
Pallas, V.
影响因子：
3.8
作者：
Ambrós, S;Hernández, C;Flores, R
通讯作者：
Flores, R
DOI：
10.1073/pnas.85.23.9128
发表时间：
1988-12-01
影响因子：
11.1
作者：
BRANCH, AD;BENENFELD, BJ;ROBERTSON, HD
通讯作者：
ROBERTSON, HD
影响因子：
11.4
作者：
Bouche, Nicolas;Lauressergues, Dominique;Vaucheret, Herve
通讯作者：
Vaucheret, Herve
影响因子：
7.4
作者：
Eamens, Andrew;Wang, Ming-Bo;Waterhouse, Peter M.
通讯作者：
Waterhouse, Peter M.