The role of FIS protein in the physiological control of the expression of the Escherichia coli meta-hpa operon

Abstract

Expression from the Escherichia coli W meta-hpa operon promoter (Pg) is under a strict catabolic repression control mediated by the cAMP-catabolite repression protein (CRP) complex in a glucose-containing medium. The Pg promoter is also activated by the integration host factor (IHF) and repressed by the specific transcriptional regulator HpaR when 4-hydroxyphenylacetate (4HPA) is not present in the medium. Expression from the hpa promoter is also repressed in undefined rich medium such as LB, but the molecular basis of this mechanism is not understood. We present in vitro and in vivo studies to demonstrate the involvement of FIS protein in this catabolic repression. DNase I footprinting experiments show that FIS binds to multiple sites within the Pg promoter. FIS-site I overlaps the CRP-binding site. By using an electromobility shift assay, we demonstrated that FIS efficiently competes with CRP for binding to the Pg promoter, suggesting an antagonist/competitive mechanism. RT-PCR showed that the Pg repression effect is relieved in a FIS deleted strain. The repression role of FIS at Pg was further demonstrated by in vitro transcription assays. These results suggest that FIS contributes to silencing the Pg promoter in the exponential phase of growth in an undefined rich medium when FIS is predominantly expressed.

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

“…Remarkably for Fis, there is no similarity between the two datasets either at the level of binding signals or bound genes (31% of bound genes in the Grainger dataset are recovered). This might be a consequence of differences in experimental conditions, which might affect Fis more than H-NS because of the former's link with catabolite repression (53,54); in fact, we observe a statistically significant overlap (Fisher’s exact test P  = 9.8 × 10 −6 ) between operons bound in their upstream regions by Fis (but not H-NS) in our study and publicly-available targets of CRP (14,41), the global regulator of catabolite repression. However, we note that there is only a limited correlation in binding signals between the studies of Cho et al .…”

“…performed theirs in M9 minimal medium plus fructose. This could have led to substantial differences in Fis binding profiles due to its reported association with catabolite repression and competition with the global transcription factor CRP (53,54). Analysis performed here shows statistically significant overlap between Fis-bound genes and known CRP targets.…”

RpoS integrates CRP, Fis, and PhoP signaling pathways to control Salmonella Typhi hlyE expression

“…Fis (factor for inversion simulation) is a nucleoid-associated protein that participates in the structuring of the bacterial chromosome, also known to interact at specific promoters to regulate gene transcription in E. coli and S. enterica [17-19]. Since Fis has been implicated in catabolite repression in E. coli [20,21], we assessed the role of Fis in hlyE transcription in S. Typhi by RT-PCR. As shown in Figure 1A, the Δ fis mutant presented increased transcription of hlyE compared with the WT, similar to the levels detected in the Δ crp mutant (control).…”

Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA

“…ArcA is a known regulator of oxygen response and respiration in MR-1 ,2,35,36 and is, therefore, a plausible co-regulator with CRP in gene transcription. Recent studies also suggest that epigenetic factors involving histone-like proteins, such as FIS, HNS, and IHF, are involved in transcriptional control by CRP 37–39. These observations led us to examine the co-regulatory effects of ArcA and IHF on CPR IGA.…”