Jagtap Soham, Shivaprasad Padubidri V
National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, India.
BMC Genomics. 2014 Dec 2;15(1):1049. doi: 10.1186/1471-2164-15-1049.
Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved.
We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.
Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.
微小（mi）RNA是植物发育的重要调节因子。在整个植物谱系中，类Dicer 1（DCL1）蛋白逐步加工长双链样结构以产生微小（mi）RNA双链体。这些miRNA被整合到AGO蛋白中，并影响与miRNA具有序列互补性的RNA的表达。植物对AGO的表达水平进行严格调控，以尽量减少使用miRNA靶向编码AGO的mRNA时产生不必要的干扰。AGO也可能具有高度的启动子特异性——有时AGO的表达可能仅限于植物中的少数细胞。病毒病原体利用各种手段对抗AGO的抗病毒作用，包括劫持宿主编码的miRNA来靶向AGO。在模式植物拟南芥中已经描述了两种宿主编码的靶向AGO的miRNA，即miR168和miR403，并且由于AGO序列高度保守，这种机制被认为在整个植物中都得到了很好的保留。
我们表明，由于靶向AGO的两种miRNA序列的多样性、AGO mRNA中相应靶区域之间的序列多样性以及这些miRNA在维管植物中的可变表达水平，AGO mRNA与miRNA之间的相互作用具有物种特异性。我们使用了代表31个植物科的68种植物的miRNA序列进行此分析。miR168和miR403的序列在植物谱系中并不保守，但令人惊讶的是，即使在亲缘关系密切的植物中，它们的序列多样性和表达水平也有很大差异。植物中miR168表达的变化与其前体的二级结构/环序列长度密切相关。
我们的数据表明，由于miRNA序列多样性和AGO mRNA中miRNA靶向区域的序列，植物谱系之间存在复杂的AGO靶向相互作用，因此导致这样一种假设，即利用宿主miRNA靶向抗病毒AGO的病毒所造成的干扰只能是物种特异性的。我们还表明，烟草中miR168亚型的快速进化和可能的表达缺失与MITE样转座子插入miRNA和miRNA*序列之间有关，这是一种可能的机制，表明了即使其他近缘植物中有大量表达的miRNA，miRNA在少数植物谱系中是如何丢失的。
