LexA repressor and iron uptake regulator from <i>Escherichia coli</i>: new members of the CAP-like DNA binding domain superfamily

Sander, Chris; Rüterjans, Heinz; Schnarr, Manfred; Fogh, Rasmus H.; Boelens, Rolf; Kaptein, Robert

doi:10.1093/protein/7.12.1449

Cited by 39 publications

(21 citation statements)

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“…However, both proteins are dimeric, HTH-containing DNA-binding proteins thought to be related to the same superfamily of regulators (the CAP/LexA superfamily) (19,25). While DtxR has been the subject of numerous structural studies performed with X-ray crystallography, a structure has yet to be reported for any member of the Fur family.…”

Section: Stoichiometry Of Fur-dna Complexesmentioning

confidence: 99%

Recognition of DNA by Fur: a Reinterpretation of the Fur Box Consensus Sequence

2002

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Ferric uptake repressor (Fur) proteins regulate the expression of iron homeostasis genes in response to intracellular iron levels. In general, Fur proteins bind with high affinity to a 19-bp inverted repeat sequence known as the Fur box. An alignment of 19 operator sites recognized by Bacillus subtilis Fur revealed a different conserved 15-bp (7-1-7) inverted repeat present twice within this 19-bp consensus sequence. We demonstrated using electrophoretic mobility shift assays that this 7-1-7 inverted repeat comprises a minimal recognition site for high-affinity binding by Fur. The resulting revised consensus sequence is remarkably similar to a related 7-1-7 inverted repeat sequence recognized by PerR, a Fur paralog. Our analysis of the affinity and stoichiometry of DNA binding by B. subtilis Fur, together with a reinterpretation of previously described studies of Escherichia coli Fur, supports a model in which the 19-bp Fur box represents overlapping recognition sites for two Fur dimers bound to opposite faces of the DNA helix. The resulting recognition complex is reminiscent of that observed for the functionally related protein DtxR. Like Fur, DtxR contains a helix-turn-helix DNAbinding motif, recognizes a 19-bp inverted repeat sequence, and has a typical DNase I footprint of ϳ30 bp. By envisioning a similar mode of DNA recognition for Fur, we can account for the internal symmetries noted previously within the Fur box, the tendency of Fur to extend into adjacent regions of DNA in a sequenceselective manner, and the observed patterns of DNA protection against enzymatic and chemical probes.

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Section: Stoichiometry Of Fur-dna Complexesmentioning

confidence: 99%

Recognition of DNA by Fur: a Reinterpretation of the Fur Box Consensus Sequence

2002

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“…The mechanism by which the Fur protein actually represses P1 is not trivial, however. Fur is a somewhat unusual DNA-binding protein as it is devoid of conventional helix-turn-helix motifs (Pabo and Sauer, 1984;Holm et al, 1994) and displays a mechanism of sequence-specific recognition that involves the extension of the N-terminal domain to reach out to the DNA (Coy and Neilands, 1991). In addition to this, Fur seems to polymerize around the DNA of the aerobactin promoter with a precise directionality but unclear stoichiometry.…”

Section: Introductionmentioning

confidence: 99%

Metalloregulation in vitro of the aerobactin promoter of Escherichia coli by the Fur (ferric uptake regulation) protein

Escolar

Lorenzo

Pérez-Martı́n

1997

Molecular Microbiology

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SummaryThe mechanism of transcriptional repression of the aerobactin operon of Escherichia coli by the Fe 2þ -responsive Fur (ferric uptake regulation) protein has been investigated. In the presence of a divalent metal, such as Mn 2þ , the Fur protein sequentially occupies two defined sites at the aerobactin promoter region, followed by a looser occupation of upstream DNA sequences. However, binding to the primary target site suffices for the entire repression effect. Comparison of transcription patterns generated with run-off experiments in the presence and absence of heparin showed that access of the RNA polymerase to the principal ¹35/¹10 hexamers of the promoter region was fully prevented by Fur-Mn 2þ bound to its primary site. Similarly, promoter-bound RNA polymerase could not be competed out from the DNA even in the presence of a large Fur-Mn 2þ excess, although the repressor could immediately bind its target sequence at the region as soon as RNA polymerase moved away from the promoter during transcription. The high affinities of either protein for the promoter produce, in practice, a first-come, first-served effect that helps the system to respond instantly to changes in the iron status of the cells.

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“…Fur was first discovered in the gram-negative bacteria Salmonella and Escherichia coli (5,13), in which it is responsible for specific regulation of many genes involved in iron metabolism. The E. coli Fur protein is a dimeric DNA binding protein related to the CAP family (18). Each 17-kDa monomer contains an N-terminal DNA binding motif and a C-terminal metal binding domain.…”

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confidence: 99%

Unusual Regulatory Elements for Iron Deficiency Induction of the idiA Gene of Synechococcus elongatus PCC 7942

2001

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Expression of a thylakoid membrane-associated protein called IdiA (iron-deficiency-induced protein A) is highly elevated and tightly regulated by iron limitation in Synechococcus elongatus PCC 6301 and PCC 7942. Although this protein is not essential for photosystem II (PSII) activity, it plays an important role in protecting the acceptor side of PSII against oxidative damage, especially under iron-limiting growth conditions, by an unknown mechanism. We defined the iron-responsive idiA promoter by using insertional inactivation mutagenesis and reporter gene assays. A 67-bp DNA region was sufficient for full iron deficiency-inducible idiA promoter activity. Within this fragment is a palindromic sequence 4 bp upstream of a putative ؊35 promoter element, which resembles the binding site of FNR/CAP-type helix-turn-helix transcription factors. The absence of this palindromic sequence or a 3-bp mutation in a putative ؊10 region eliminated promoter activity completely. A previously identified candidate for a positively acting transcription factor is the IdiB protein, whose gene lies immediately downstream of idiA. IdiB shows strong similarity to helix-turn-helix transcription factors of the FNR/CAP family. A His 6x -tagged IdiB that was overexpressed in Escherichia coli bound to a 59-bp fragment of the idiA regulatory region that included the palindrome. Although the idiA promoter lacks a consensus binding site for the iron-sensing regulator Fur, we attempted to inactivate fur in order to investigate the potential role of this factor. The resulting merodiploid mutants showed constitutive partial derepression of IdiA expression under iron-sufficient growth conditions. We concluded that IdiB is a specific iron-responsive regulator of idiA and that Fur has an indirect role in influencing idiA expression.

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LexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily

Cited by 39 publications

References 0 publications

Recognition of DNA by Fur: a Reinterpretation of the Fur Box Consensus Sequence

Recognition of DNA by Fur: a Reinterpretation of the Fur Box Consensus Sequence

Metalloregulation in vitro of the aerobactin promoter of Escherichia coli by the Fur (ferric uptake regulation) protein

Unusual Regulatory Elements for Iron Deficiency Induction of the idiA Gene of Synechococcus elongatus PCC 7942

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