Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria

Abstract

In the ancient anaerobic environment, ferrous iron (Fe(2+)) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe(3+)) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe(3+), bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe(3+). However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe(2+) as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.

Keywords: Ferric Uptake Regulator; gene regulation; iron; oxidative stress; pathogenic bacteria.

Figure 1

The classic model of Fur repression of iron acquisition (iucA as an example). (A) Biosynthesis of the siderophore aerobactin requires several genes located in an operon (iucABCD, iutA). Expression of the initial gene, iucA, is Fur-repressed (De Lorenzo et al., 1987) and production of aerobactin is known to be produced by virulent strains of bacteria, especially strains causing disease in avian hosts (i.e., Avian pathogenic E. coli or APEC) (Lafont et al., ; Xiong et al., ; Ling et al., 2013). The sequential enzymatic activity of IucD, IucB, IucC, and IucA convert L-lysine into aerobactin, a potent Fe-scavenging siderophore. (B) There are two Fur-binding sites (FBS) for Fe-dependent regulation of iucA. Both FBS are located within the P1 promoter (overlapping the −35 and also the −10 sites). Under conditions of Fe-deprivation (left panel), there is increased transcription (signified by a +1) of the iucABCD genes whose protein products form a biosynthetic pathway that produces aerobactin. Under Fe-replete conditions (right panel), Fur binds to DNA at the FBS (green box) and blocks access of the −35 and −10 sites by RNA polymerase (RNAP, blue shape).

Figure 2

Models of the Fur-dependent activation of gene expression in bacteria. (A) Fur activation through “ryhB-dependent” mechanism (SodB as an example). Fur is indirectly required for the expression of the FeSOD (SodB) in bacteria through the sRNA ryhB (Masse and Gottesman, ; Ellermeier and Slauch, 2008). Under conditions of Fe²⁺ depletion (top panel), Fur is unable to directly repress transcription of the sRNA ryhB (or its paralog). This results in an increase in the level of ryhB within the cell. The RNA chaperone Hfq binds to ryhB and to the target mRNA of sodB (Afonyushkin et al., ; Urban and Vogel, 2007), which through the RNase-dependent cleavage (cleavage sites are signified by filled triangles) reduces the half-life of sodB mRNA and reduces SodB protein within the cell. The Fur activation of sodB is diminished in the absence of Hfq or ryhB (Masse and Gottesman, ; Ellermeier and Slauch, ; Troxell et al., 2011a). When Fur is activated during Fe²⁺ replete conditions (bottom panel), transcription of ryhB is blocked, which increases the half-life of sodB mRNA allowing for enhanced production of SodB protein and FeSOD activity. (B) Fur activation through “RNAP recruitment” mechanism (Examples from S. Typhimurium and H. Pylori). In vitro transcription assays with H. pylori norB regulatory sequences (Delany et al., 2004) and S. Typhimurium hilD regulatory sequences (Teixido et al., 2011) demonstrate an active Fur-Fe²⁺ binding to a FBS (signified with a green box) that promotes increased binding of the RNAP (signified with a blue shape) to the promoter and transcription of the target gene (signified with a +1). In both examples, the regulatory sequences of norB and hilD contain a repression site (signified with a red box) that may overlap the FBS (an ArsR-binding site with norB) or be located immediately downstream of the FBS (an H-NS binding site with hilD). If Fur-Fe²⁺ physically contacts the RNAP is unknown. (C) Fur activation through “antirepressor” mechanism (FtnA as an example). In E. coli, expression of the ftnA gene is Fur activated, but independent of the “ryhB-dependent” activation. Under Fe²⁺ poor conditions, H-NS binds upstream of the ftnA gene and represses transcription (top panel). When Fur is activated, Fur-Fe²⁺ binds to several FBS located upstream of ftnA, which prevents H-NS nucleation at the ftnA promoter and repressing transcription (bottom panel). In this example, Fur is required to block H-NS binding and can physically remove H-NS from the upstream regulatory site, which allows for ftnA expression.