Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains.
Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains.
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DOI：
10.1111/mmi.12748
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发表时间：
2014-10
影响因子：
3.6
通讯作者：
Bechhofer DH
中科院分区：
文献类型：
--
作者：
Liu B;Deikus G;Bree A;Durand S;Kearns DB;Bechhofer DH
枯草芽孢杆菌中的信使RNA降解是通过核糖核酸外切酶和核糖核酸内切酶的组合完成的。衰变过程中的中间体还不容易检测到，以前对mRNA衰变的研究使用了少数高度表达的转录本作为模型。在这里，我们使用RNA-Seq分析在全球范围内探测mRNA周转。相当一部分的信息显示了定位在编码序列的5'或3'末端附近的RNA片段的差异积累，这与从5'末端或从内部切割位点开始衰变一致。将野生型中的mRNA降解模式与缺乏多核苷酸磷酸化酶（PNIPs）的突变株中的模式进行比较，PNIPs被认为是mRNA降解中的主要3'外切核酸酶活性，并且是B中四种已知的3'外切核酸酶之一。枯草杆菌。结果表明，在许多情况下，mRNA周转对PNIPs有显著的依赖性，这表明3'外切核酸酶从3'-羟基末端降解的能力具有特异性。RNA-Seq数据证明了PNPase-deletion菌株中Sigma D表达的急剧降低。sigD调节子表达的减少解释了PNTR突变体的链生长表型，也预测了群集运动的缺陷。
Messenger RNA decay in Bacillus subtilis is accomplished by a combination of exoribonucleases and endoribonucleases. Intermediates in the decay process have not been readily detectable, and previous studies on mRNA decay have used a handful of highly expressed transcripts as models. Here, we use RNA-Seq analysis to probe mRNA turnover globally. A significant fraction of messages showed differential accumulation of RNA fragments that mapped near the 5’ or 3’ end of the coding sequence, consistent with initiation of decay from either the 5’ end or from an internal cleavage site. Patterns of mRNA decay in the wild type were compared with patterns in a mutant strain lacking polynucleotide phosphorylase (PNPase), which is considered the major 3’ exonuclease activity in mRNA decay and which is one of four known 3’ exonucleases in B. subtilis. The results showed a striking dependence on PNPase for mRNA turnover in many cases, suggesting specificity in the ability of 3’ exonucleases to degrade from 3’-hydroxyl termini. RNA-Seq data demonstrated a sharp decrease in expression of Sigma D in the PNPase-deletion strain. Reduction in sigD regulon expression explained the chain growth phenotype of the PNPase mutant and also predicted a defect in swarming motility.
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