Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Planegg-Martinsried, 82152, Germany.
Department Biologie, Bereich Theoretische Biophysik, Humboldt-Universität Berlin, Berlin, 10115, Germany.
Plant J. 2020 Sep;104(1):138-155. doi: 10.1111/tpj.14912. Epub 2020 Jul 22.
Chloroplast perturbations activate retrograde signalling pathways, causing dynamic changes of gene expression. Besides transcriptional control of gene expression, different classes of small non-coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling are lacking. We performed sRNA profiling in response to norflurazon (NF), which provokes retrograde signals, in Arabidopsis thaliana wild type (WT) and the two retrograde signalling mutants gun1 and gun5. The RNA samples were also used for mRNA and long non-coding RNA profiling to link altered sRNA levels to changes in the expression of their cognate target RNAs. We identified 122 sRNAs from all known sRNA classes that were responsive to NF in the WT. Strikingly, 142 and 213 sRNAs were found to be differentially regulated in both mutants, indicating a retrograde control of these sRNAs. Concomitant with the changes in sRNA expression, we detected about 1500 differentially expressed mRNAs in the NF-treated WT and around 900 and 1400 mRNAs that were differentially regulated in the gun1 and gun5 mutants, with a high proportion (~30%) of genes encoding plastid proteins. Furthermore, around 20% of predicted miRNA targets code for plastid-localised proteins. Among the sRNA-target pairs, we identified pairs with an anticorrelated expression as well pairs showing other expressional relations, pointing to a role of sRNAs in balancing transcriptional changes upon retrograde signals. Based on the comprehensive changes in sRNA expression, we assume a considerable impact of sRNAs in retrograde-dependent transcriptional changes to adjust plastidic and nuclear gene expression.
叶绿体扰动激活逆行信号通路，导致基因表达的动态变化。除了基因表达的转录控制外，不同类别的小非编码 RNA（sRNA）也在基因表达控制中起作用，但缺乏关于它们在逆行信号中的作用的综合分析。我们在拟南芥野生型（WT）和两个逆行信号突变体 gun1 和 gun5 中对引发逆行信号的 norflurazon（NF）进行了 sRNA 分析。还使用这些 RNA 样品进行 mRNA 和长非编码 RNA 分析，将改变的 sRNA 水平与它们同源靶 RNA 表达的变化联系起来。我们从所有已知的 sRNA 类别中鉴定出 122 个对 NF 在 WT 中响应的 sRNA。引人注目的是，在两个突变体中都发现了 142 和 213 个 sRNA 差异调节，表明这些 sRNA 受到逆行控制。伴随着 sRNA 表达的变化，我们在 NF 处理的 WT 中检测到约 1500 个差异表达的 mRNA，而在 gun1 和 gun5 突变体中约有 900 和 1400 个 mRNA 差异调节，其中约 30%的基因编码质体蛋白。此外，约 20%的预测 miRNA 靶标编码质体定位蛋白。在所鉴定的 sRNA-靶标对中，我们鉴定出具有反相关表达的对以及表现出其他表达关系的对，表明 sRNA 在平衡逆行信号后转录变化中的作用。基于 sRNA 表达的综合变化，我们假设 sRNA 在逆行依赖性转录变化中具有相当大的影响，以调整质体和核基因表达。
