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PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli

机译：PNPase参与大肠杆菌稳定期细胞中mRNA的降解和表达的协调

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Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. This work had identified PNPase as a central player associated with mRNA degradation in stationary phase.
机译：外切核糖核酸酶对于大肠杆菌中的RNA降解至关重要，但RNase R和PNPase的作用以及它们在固定相中的潜在重叠尚不明确。在这里，我们使用了全基因组方法来确定RNase R和PNPase如何影响固定相中的mRNA半衰期。通过对转录停滞后的转录组进行动态分析来确定全基因组mRNA的半衰期。我们将mRNA半衰期的分析与稳态浓度（转录组）相结合，以提供这些外切核糖核酸酶在基因组规模上的体内活性的综合概述。 mRNA半衰期的值表明，mRNA在固定相中非常稳定，RNase R或PNPase的缺失仅引起有限的mRNA稳定。有趣的是，缺乏PNPase还会引起许多mRNA的不稳定。 PNPase缺失菌株中mRNA半衰期的这些变化与mRNA水平的大规模重组以及几种ncRNA浓度的变化有关。最后，与RNase R突变体不同，发现PNPase突变体中的降解机制的体内活性经常被mRNA饱和，这表明降解活性受PNPase缺失的限制，但不受RNase R缺失的限制。已确定PNPase是与固定相中mRNA降解相关的中心参与者。

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