RNA-seq based transcriptional profiling of petroleum sludge-derived Pseudomonas aeruginosa ZS1 strain in response to alteration of growth conditions. RNA-seq based transcriptional profiling of petroleum sludge-derived Pseudomonas aeruginosa ZS1 strain in response to alteration of growth conditions

We show that ZS1 in the medium supplemented with YE (YE-medium) produces more cell biomass but less rhamnolipid than it does in Glc-medium. To elucidate the transcriptional regulation of genes that are involved in biosynthesis of rhamnolipids and its precursors, RNA-seq-based transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-media is performed. Based on the assembly of ZS1 transcriptome using the reference PAO1 genome, we show that genes involved in energy metabolic pathways in ZS1 strain are highly transcribed in YE medium but not in Glc-medium, in agreement with their cell mass production. Similarly, transcription of quorum sensing systems genes lasI-lasR, rhlI-rhlR, and pqsH-mvfR are downregulated in Glc-medium. On the other hand, we show that two of the three enzymes RhlB and RhlC essential for rhamnolipid biosynthesis are transcriptionally upregulated, independent of quorum sensing signals. Notably, three of the four enzymes involved in dTDP-L-rhamnose, a precursor for the rhamnolipid biosynthesis, are downregulated in Glc except for RmlD that catalyzes the last reaction in the pathway. Together, our results indicate that increased rhamnolipid production in ZS1 cells is independent of quorum sensing signals. We propose that quorum sensing-independent rhamnolipid production in ZS1 Glc-culture is achieved by transcriptional re-programming of the minimum number of genes involved in rhamnolipid biosynthesis. Overall design: Examination of transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-medium.

我们发现，在添加YE的培养基（YE-medium）中培养的ZS1菌株，其细胞生物量高于Glc培养基（Glc-medium）培养的菌株，但鼠李糖脂（rhamnolipid）产量更低。为阐明参与鼠李糖脂及其前体生物合成的基因的转录调控规律，本研究对经YE与Glc培养基互换培养的ZS1细胞开展了基于RNA测序（RNA-seq）的转录组分析。以PAO1参考基因组（PAO1 genome）为参照组装ZS1转录组后，我们发现ZS1菌株的能量代谢通路相关基因在YE培养基中呈高转录水平，而在Glc培养基中则无此现象，这与其细胞生物量的生成情况一致。同理，群体感应（quorum sensing）系统基因lasI-lasR、rhlI-rhlR及pqsH-mvfR的转录在Glc培养基中均被下调。另一方面，我们发现参与鼠李糖脂生物合成的三种关键酶中的两种——RhlB与RhlC——的转录水平被上调，且该调控不依赖于群体感应信号。值得注意的是，参与鼠李糖脂生物合成前体dTDP-L-鼠李糖（dTDP-L-rhamnose）合成的四种酶中，有三种在Glc培养基中被下调，唯有催化该通路最后一步反应的RmlD除外。综合来看，我们的研究结果表明，ZS1细胞中鼠李糖脂产量的提升不依赖于群体感应信号。我们提出，在ZS1的Glc培养体系中，不依赖群体感应的鼠李糖脂生成，是通过对参与鼠李糖脂生物合成的少量核心基因进行转录重编程实现的。实验整体设计：分析经YE与Glc培养基互换培养的ZS1细胞的转录组特征。