Global transcriptome changes after nitrogen replenishment in S288c yeast strain

The study on the effect of nitrogen replenishment on the gene expression showed that 390 genes were significantly upregulated (with a logFC ranging from 4.5 to 0.8), among which those related to RNA binding, ribosome binding, structural constituent of ribosome, transferase activity and transcription. 833 genes were significantly down-regulated (with a logFC ranging from -0.8 to -5.2) including those related to stress response, amino-acid catabolism process, protein catabolic process (ubiquitin-dependent and vacuolar protein degradation). But the most interesting and unexpected changes were those related to the down-regulation of the glycolytic transcripts. In fact, we observed a rapid down-regulation of many glycolytic mRNA (25/34) 30 min after nitrogen repletion. These data were surprising as expression of the glycolytic genes are generally considered as stable and sometimes they are even used as housekeeping control genes. In addition, the decoupling of the glycolytic gene expression from the expression of RP genes, ribosomal genes or those related to protein synthesis is unique to the present dataset as in most other data expression of these groups are tightly correlated when nutrients are available. This prompts us to examine in some details the factors which led to the control of the glycolytic mRNA instability in conditions of nitrogen replenishment.本研究针对氮补充对基因表达的影响开展分析，结果显示共有390个基因出现显著上调（logFC范围为4.5至0.8），其中涉及RNA结合、核糖体结合、核糖体结构组分、转移酶活性及转录过程相关基因；另有833个基因发生显著下调（logFC范围为-0.8至-5.2），涵盖应激反应、氨基酸分解代谢过程、蛋白质分解代谢过程（泛素依赖型及液泡型蛋白质降解）相关基因。但最引人关注且出乎意料的变化，与糖酵解转录本的下调有关。实际上，我们观察到在氮补充后30分钟，多数糖酵解mRNA（25/34）出现了快速下调。该结果令人意外，因为糖酵解基因的表达通常被认为是稳定的，部分情况下甚至可作为管家对照基因（housekeeping control genes）使用。此外，糖酵解基因表达与RP基因（Ribosomal Protein genes）、核糖体基因或蛋白质合成相关基因表达的解耦现象，为本数据集所独有——在多数其他研究数据中，当营养物质充足时，这类基因群的表达通常呈紧密相关状态。这促使我们深入探究氮补充条件下，调控糖酵解mRNA稳定性的相关因素。