Aberg Anna, Fernández-Vázquez Jorge, Cabrer-Panes Juan David, Sánchez Alex, Balsalobre Carlos
Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden.
J Bacteriol. 2009 May;191(10):3226-36. doi: 10.1128/JB.01410-08. Epub 2009 Feb 27.
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 (DeltadksA). 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) DeltadksA 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.
ppGpp和DksA在转录过程中的协同作用已得到广泛记载。与该模型不同的是，表型研究表明，ppGpp和DksA在大肠杆菌的基因表达中可能也具有独立且相反的作用。在本研究中，我们采用转录组学方法比较了ppGpp缺陷型（ppGpp(0)）和/或DksA缺陷型（DeltadksA）菌株中基因表达的全局转录模式。在ppGpp缺陷型和DksA缺陷型菌株中，分别约有6%和7%的所有基因受到两倍以上的显著影响，在ppGpp(0) DeltadksA菌株中这一比例增至所有基因的13%。尽管数据表明大多数受影响的基因受到ppGpp和DksA的同向或反向调控，但也发现了一些由这两个因子独立和/或差异调控的基因。趋化性和鞭毛合成基因的大功能组受到显著差异影响，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。值得注意的是，抗暂停Gre因子的突变抑制了在DksA缺陷型菌株中观察到的上调，强调了RNA聚合酶二级通道对大肠杆菌基因表达调控和微调的重要性。
