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Chapter 13 : Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression

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Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, Page 1 of 2

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Abstract:

Fe binds directly to the Fur protein, which in turn, acquires a configuration capable of binding a specific DNA sequence. Although this chapter deals primarily with negative regulation by iron, it should be noted that several genes (including , , , , , , and ) and other bacteria are positively controlled by FeFur. While some of the minor divergences between the different models could be attributed to peculiarities of the Fur proteins from different origins, the ultimate understanding of the Fur-DNA interactions requires accessing the cocrystal of Fur bound to its canonical 19-bp consensus target. Regardless of the specific mechanism by which Fur binds its target DNA, it is possible to describe Fur sites in a genome as an array of the hexamer NAT(A/T)AT. This affords a new interpretation of many previously reported Fur sites. The recent availability of bacterial genomes allows massive comparisons of DNA sequences that can be the target of regulatory proteins. In particular, some Fur-binding sites and some UP elements seem to occasionally coincide in the chromosome of .

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13

Key Concept Ranking

Gene Expression and Regulation
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Transcription Start Site
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DNA Synthesis
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Outer Membrane Proteins
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Figures

Image of FIGURE 1
FIGURE 1

Standard model of Fur-mediated repression of metallo-regulated genes. Under iron-rich conditions, Fur binds the divalent ion, acquires a configuration able to bind target DNA sequences (generally known as Fur boxes or iron boxes [ Fig. 4 ]), and inhibits transcription from virtually all the genes and operons repressed by the metal. In contrast, when iron is scarce, the equilibrium is displaced to release Fe, the RNA polymerase accesses cognate promoters, and the genes for the biosynthesis of siderophore and other iron-related functions are expressed. In some cases (notably in ), Fur controls the expression of at least one dedicated sigma factor (PvdS), which, in turn, causes a discrete set of genes to be expressed.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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Image of FIGURE 2
FIGURE 2

Organization of the promoter region in . The noncoding DNA upstream and downstream area of the nearby and genes is enlarged. Sites for binding of each relevant regulatory protein (SoxS, OxyR, Fur, and the predicted catabolite activation protein [CAP]) are indicated (the size and stoichiometry are symbolic), as well as the transcription start site from each of the promoters. Note that can be expressed through a weak downstream promoter, (), modulated by CAP and Fur or by a strong OxyR-activated promoter, (), located further upstream. Finally, can be cotranscribed with from a still further upstream SoxS-activated promoter.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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Image of FIGURE 3
FIGURE 3

Domain structure of the Fur protein of . The sketch at the top is based on Pohl et al. (2003). The FurPA protein clearly has two domains: an N-terminal DNA-binding module (structurally similar to that of DtxR), and a distinct dimerization domain. The two modules are linked by a peptide, which is arranged around a permanently bound Zn atom. This important atom at metal-binding site 2 assists proper positioning between the DNA-binding and dimerization modules. The site for the regulatory divalent metal ion (presumably iron in vivo) is called site 1 and is occupied by Zn in the FurPA protein crystal. The ion at site 1 is coordinated by two residues following the loop that links the DNA-binding and dimerization domains. Metal binding could lead to a conformational change at this location, resulting in a motion changing the relative orientation of the DNA-binding domains of the dimer and thus increasing the affinity for the target DNA sequence. The drawings at the bottom symbolize the differences between the relative orientations of the otherwise very similar DNA-binding domains of FurPA and DtxR.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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Image of FIGURE 4
FIGURE 4

Interpretation of the canonical or consensus 19-bp Fur box as an array of hexameric sequences. The scheme shows alternative interpretations of the 19-bp consensus Fur-binding site (Fur box) in These include a palindromic sequence composed of two 9-bp inverted repeats, an array of three directed 6-bp repeats, with the third repeat being imperfect, or an array of two directed repeats and one inverted repeat of the invariable sequence GATAAT.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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Image of FIGURE 5
FIGURE 5

Interpretation of the consensus Fur-binding site as two overlapping palindromes that are recognized at opposite sides of the DNA helix. This model can accommodate a minimal recognition sequence of 21 bp [2 × (7–1–7)] or a shorter segment [2 × (6–1–6)]. The lower part of the figure indicates how the primary binding site would be assembled. Note that the central portion of the sequence is bound simultaneously at the two somewhat opposite sides of the helix.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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Image of FIGURE 6
FIGURE 6

View of iron-responsive promoters of as arrays of hexameric sequences. The promoters shown here include those of the siderophore systems aerobactin () and enterochelin (, , and ), as well as those of the gene itself, the receptor for colicin I (), and the receptor for superoxide dismutase (). The three repeats which comprise the consensus Fur box include the most highly conserved sequences. However, in addition, many other conserved bases [according to the 6-bp minimal motif NAT(A/T)AT discussed in the text] can be found within the protected sequences neighboring the core Fur box. It is likely that such adjacent sequences are not coincidental but are arrayed in a configuration of 6-bp repeats with a potential to interact specifically with the Fur protein as a whole. These additional contacts might strengthen the overall binding of the DNA segment to the regulator and explain why the protection is not limited to the consensus Fur box. It seems, therefore, that once a minimum of three repeats is assembled, a further increase in the number of repeats, in any orientation, may extended Fur-binding sites with higher affinities for the protein resulting from their increasingly cooperative occupation.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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Image of FIGURE 7
FIGURE 7

Fur boxes and UP elements. The figure shows an alignment between the consensus UP site and the Fur box. W = A or T; R = A or G; N = any base. If the same UP-like site is occupied by Fur- Mn (in vitro) or Fur-Fe2_ (in vivo), the RNAP may fail to bind the downstream -10 and -35 hexamers. In this way, Fur would hinder the UP-like element created by its own recognition sequence.

Citation: de Lorenzo V, Perez-Martín J, Escolar L, Pesole G, Bertoni G. 2004. Mode of Binding of the Fur Protein to Target DNA: Negative Regulation of Iron-Controlled Gene Expression, p 185-196. In Crosa J, Mey A, Payne S, Iron Transport in Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816544.ch13
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References

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