Ribonuclease E strongly impacts bacterial adaptation to different growth conditions

Adaptation of bacteria to changes in their environment is often accomplished by changes of the transcriptome. While we learned a lot on the impact of transcriptional regulation in bacterial adaptation over the last decades, much less is known on the role of ribonucleases. This study demonstrates an important function of the endoribonuclease RNase E in the adaptation to different growth conditions. It was shown previously that RNase E activity does not influence the doubling time of the facultative phototroph <i>Rhodobacter sphaeroides</i> during chemotrophic growth, however, it has a strong impact on phototrophic growth. To better understand the impact of RNase E on phototrophic growth, we now quantified gene expression by RNA-seq and mapped 5’ ends during chemotrophic growth under high oxygen or low oxygen levels and during phototrophic growth in the wild type and a mutant expressing a thermosensitive RNase E. Based on the RNase E-dependent expression pattern, the RNAs could be grouped into different classes. A strong effect of RNase E on levels of RNAs for photosynthesis genes was observed, in agreement with poor growth under photosynthetic conditions. RNase E cleavage sites and 5’ ends enriched in the <i>rne</i>^<i>ts</i> mutant were differently distributed among the gene classes. Furthermore, RNase E affects the level of RNAs for important transcription factors thus indirectly affecting the expression of their regulons. As a consequence, RNase E has an important role in the adaptation of <i>R. sphaeroides</i> to different growth conditions.

细菌对环境变化的适应通常通过转录组的改变来实现。尽管近数十年来，我们对转录调控在细菌适应过程中的作用已有诸多认知，但关于核糖核酸酶（ribonucleases）所扮演的角色，我们的了解仍十分有限。本研究揭示了核糖核酸内切酶RNase E（endoribonuclease RNase E）在适应不同生长条件中的重要功能。此前已有研究表明，在化能营养生长阶段，RNase E的活性并不会影响兼性光养细菌球形红杆菌（Rhodobacter sphaeroides）的倍增时间，但其对光养生长却有着显著影响。为深入解析RNase E对光养生长的影响，本研究通过RNA-seq技术对基因表达进行定量分析，并绘制了高氧、低氧条件下化能营养生长阶段，以及野生型与表达热敏型RNase E的突变株的光养生长阶段的5’端图谱。基于RNase E依赖的表达模式，这些RNA可被划分为不同类别。研究观察到RNase E对光合作用相关基因的RNA水平具有极强调控作用，这与光合条件下生长不良的表型相一致。在rne^ts突变体中富集的RNase E剪切位点与5’端，在不同基因类别中的分布存在显著差异。此外，RNase E还会影响重要转录因子对应的RNA水平，从而间接调控其调节子（regulons）的表达。综上，RNase E在球形红杆菌（R. sphaeroides）适应不同生长条件的过程中发挥着关键作用。