Investigation on the anaerobic propionate degradation by Escherichia coli K12. Escherichia coli K-12

Propionate is an abundant carboxylic acid in nature. Microorganisms metabolize propionate aerobically via the 2-methylcitrate pathway. This pathway depends on a series of three reactions in the citric acid cycle that leads to the conversion of succinate to oxaloacetate. Interestingly, the gamma-proteobacterium Escherichia coli can use propionate as a carbon and electron source under oxic but not under anoxic conditions. The typical downregulation of the citric acid cycle under anoxic conditions is only partially responsible for the inability to use propionate under anoxic conditions since an arcA mutant shows very limited growth on propionate. RT-PCR and transcriptomic analysis revealed a post-transcriptional regulation of the prp-genecluster encoding the necessary enzymes for propionate metabolism. The polycistronic mRNA was hydrolyzed in the 3`-5` direction under anoxic conditions. This regulatory strategy is highly constructive because the last gene of the operon encodes the first enzyme of the propionate metabolism. Further analysis revealed that RNase R catalyzes the hydrolysis of the prp transcripts. Consequently, an rnr-deletion strain could metabolize propionate under anoxic conditions. To the best of our knowledge, this is the first study describing the influence of RNase R on the anaerobic metabolism of E. coli. Overall design: RNA-seq of E. coli K12 wild type and delta-rnr mutant under aerobic and anaerobic growth with and without propionate. Duplicate samples for each condition.

丙酸（propionate）是自然界中广泛分布的羧酸类化合物。微生物可通过2-甲基柠檬酸途径（2-methylcitrate pathway）需氧代谢丙酸。该途径依赖三羧酸循环中介导琥珀酸向草酰乙酸转化的三步连续反应。值得注意的是，γ-变形菌门的大肠杆菌（Escherichia coli）可在有氧条件下以丙酸作为碳源与电子供体，但无法在厌氧条件下利用丙酸。厌氧条件下三羧酸循环的典型下调仅能部分解释大肠杆菌无法在厌氧条件下利用丙酸的现象，因为arcA突变体在丙酸培养基上的生长仅极为有限。逆转录PCR（RT-PCR）与转录组分析结果显示，编码丙酸代谢必需酶的prp基因簇（prp-genecluster）存在转录后调控。厌氧条件下，该多顺反子mRNA以3'→5'方向被水解。该调控策略具有重要的生物学意义，因为该操纵子的最后一个基因编码丙酸代谢途径的首个酶。进一步研究表明，核糖核酸酶R（RNase R）催化prp转录本的水解。因此，rnr缺失菌株可在厌氧条件下代谢丙酸。据我们所知，本研究首次阐明了RNase R对大肠杆菌厌氧代谢的调控作用。
实验整体设计：对大肠杆菌K12野生型菌株与delta-rnr突变株，在有氧、厌氧、添加丙酸、不添加丙酸的四种培养条件下开展RNA测序（RNA-seq），每个条件设置生物学重复样本。