Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus.
Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus.
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DOI：
10.1186/s12866-016-0682-y
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发表时间：
2016-04-12
期刊：
影响因子：
4.2
通讯作者：
Marques MV
中科院分区：
文献类型：
--
作者：
da Silva CA;Lourenço RF;Mazzon RR;Ribeiro RA;Marques MV
当细菌细胞进入稳定期时，它们调整其生长速率以符合营养限制并获得对几种胁迫的抗性。这些事件是通过控制基因在这个阶段的表达，改变指数增长的模式，生长停滞，并增加参与胁迫抗性的蛋白质的表达来调节。双组分系统SpdR/SpdS是新月柄杆菌cspD基因在稳定期开始时激活转录所必需的。在这项工作中，我们表明，SpdR和SpdS也被诱导进入稳定期后，这种诱导部分由ppGpp介导，它不是自动调节。通过DNA微阵列技术对spdR无效突变株与野生型菌株进行了稳定期早期的全局转录分析。23个基因在spdR缺失突变株中的表达相对于其亲本株（包括cspD）至少降低两倍，而5个基因在突变株中的表达增加。通过定量真实的时间PCR评估了一组9个基因的表达，验证了微阵列数据，并表明了SpdR在稳定期的重要作用。几个差异表达的基因可以参与调节基因表达，包括四个转录调节因子和RNA调节蛋白Hfq。核糖体蛋白NusE和NusG在转录和翻译中也具有额外的调节功能，它们在spdR突变体中以及ParE 1毒素中也被下调。电泳迁移率变动分析显示纯化的SpdR蛋白与CC 0517的调控区结合，并且显示SpdR调控的基因CC 0731在无效cspD突变体中以较低水平表达，这表明至少部分SpdR对该基因表达的影响是间接的。结果表明，SpdR调节几个基因编码的蛋白质的调节功能，这反过来可能是需要的其他基因的表达，重要的过渡到稳定期。本文的在线版本（doi：10.1186/s12866-016-0682-y）包含补充材料，可供授权用户使用。
As bacterial cells enter stationary phase, they adjust their growth rate to comply with nutrient restriction and acquire increased resistance to several stresses. These events are regulated by controlling gene expression at this phase, changing the mode of exponential growth into that of growth arrest, and increasing the expression of proteins involved in stress resistance. The two-component system SpdR/SpdS is required for the activation of transcription of the Caulobacter crescentus cspD gene at the onset of stationary phase. In this work, we showed that both SpdR and SpdS are also induced upon entry into stationary phase, and this induction is partly mediated by ppGpp and it is not auto-regulated. Global transcriptional analysis at early stationary phase of a spdR null mutant strain compared to the wild type strain was carried out by DNA microarray. Twenty-three genes showed at least twofold decreased expression in the spdR deletion mutant strain relative to its parental strain, including cspD, while five genes showed increased expression in the mutant. The expression of a set of nine genes was evaluated by quantitative real time PCR, validating the microarray data, and indicating an important role for SpdR at stationary phase. Several of the differentially expressed genes can be involved in modulating gene expression, including four transcriptional regulators, and the RNA regulatory protein Hfq. The ribosomal proteins NusE and NusG, which also have additional regulatory functions in transcription and translation, were also downregulated in the spdR mutant, as well as the ParE1 toxin. The purified SpdR protein was shown to bind to the regulatory region of CC0517 by Electrophoretic Mobility Shift Assay, and the SpdR-regulated gene CC0731 was shown to be expressed at a lower level in the null cspD mutant, suggesting that at least part of the effect of SpdR on the expression of this gene is indirect. The results indicate that SpdR regulates several genes encoding proteins of regulatory function, which in turn may be required for the expression of other genes important for the transition to stationary phase. The online version of this article (doi:10.1186/s12866-016-0682-y) contains supplementary material, which is available to authorized users.