Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli
Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli
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DOI：
10.1128/jb.01410-08
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发表时间：
2009-05-01
影响因子：
3.2
通讯作者：
Balsalobre, Carlos
中科院分区：
文献类型：
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作者：
Aberg, Anna;Fernandez-Vazquez, Jorge;Balsalobre, Carlos
ppGpp和DksA在转录中的协同行动已被广泛记录。与此模型不同的是，表型研究表明ppGpp和DksA在大肠杆菌中的基因表达中也可能具有独立和相反的作用。在这项研究中，我们使用了转录组学的方法来比较全局的基因表达的转录模式在菌株缺乏ppGpp（ppGpp（0））和/或DksA（Δ dksA）。在ppGpp和DksA缺陷型菌株中，所有基因中分别约有6%和7%受到超过两倍的显著影响，在ppGpp（0）Delta dksA菌株中增加到所有基因的13%。虽然大多数受影响的基因受ppGpp和DksA的共同或协同调控，但也发现了一些受这两种因子独立和/或差异调控的基因，其中大功能群的趋化性和鞭毛合成基因受到显著差异影响，所有基因在DksA缺陷型菌株中上调，但其中60%在ppGpp缺陷型菌株中下调。揭示性地，抗暂停Gre因子中的突变抑制了在DksA缺陷菌株中观察到的上调，强调了RNA聚合酶的二级通道对于E.杆菌
The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp(0)) and/or DksA (Delta dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp-and DksA-deficient strains, respectively, increasing to 13% of all genes in the ppGpp(0) Delta dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.