Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli

Abstract

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 (⌬dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp-and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp 0 ⌬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.

Growth Phase and (p)ppGpp Control of IraD, a Regulator of RpoS Stability, in Escherichia coli

“…The iraD gene was not found among this set but may have been missed because of growth condition differences or due to difficulty in the detection of the iraD transcript. The mechanism of this antagonistic and (p)ppGpp-independent effect by DksA on some genes appears to be competition with the GreA/B elongation factors (1,2).…”

“…However, DksA has effects on phenotypes such as adhesion, motility and chemotaxis in relA spoT double mutant strains [so-called "(p)ppGpp 0" strains] unable to synthesize (p)ppGpp (1,28), suggesting that DksA can function independently of (p)ppGpp. Microarray and fusion experiments indicated that DksA and (p)ppGpp have opposing effects on a subset of genes primarily involved in fimbriae regulation, chemotaxis and motility (1,2).…”

ppGpp Conjures Bacterial Virulence

“…However, recent studies of UPEC and E. coli K-12 have challenged the previously ascribed role of DksA during ppGpp-dependent transcriptional regulation (1,3,125). DksA not only regulates motility and cell-to-cell adhesion independently of ppGpp but also controls bacterial adherence oppositely of ppGpp (125).…”

“…Data from phenotypic studies indicate that the overproduction of DksA by ppGpp 0 bacteria can compensate for the lack of the alarmone (160). Additionally, ppGpp and DksA have opposite effects on certain E. coli traits and promoters (1,125). Furthermore, in vitro assays show opposite and independent regulations of some promoters by these two stringent response components (123,131).…”

Control of Redox Balance by the Stringent Response Regulatory Protein Promotes Antioxidant Defenses of Salmonella

“…Some of the regulatory actions of ppGpp on the activity of RNA polymerase are achieved in conjunction with DksA, a protein with structural homology to Gre transcription factors (22). However, independent and opposing roles for DksA have also been observed, supporting unique functions for DksA (23,24). DksA has been shown to play a role in the virulence of several pathogens including Salmonella; however, it is still unclear how adjustments in gene expression by DksA contribute to Salmonella pathogenesis (25).…”