Does ferredoxin I ( Azotobacter) represent a novel class of DNA-binding proteins that regulate gene expression in response to cellular iron(II)?

Abstract

Azotobacter vinelandii ( Av) and chroococcum ( Ac) ferredoxin I contain [3F-4S] 1+/0 and [4Fe-4S] 2+/1+ clusters, when isolated aerobically, which undergo one-electron redox cycles at potentials of −460±10 mV (vs SHE) at pH 8.3 and −645± 10 mV, respectively. The X-ray structure of Fd I ( Av) reveals that the N-terminal half of the polypeptide folds as a sandwich of β-strands which enclose the iron-sulphur clusters. The C-terminal sequence contains an amphiphilic α-helix of four turns which lies on the surface of the β-barrel. Fd I ( Av) controls expression of an unknown protein of M r ∼ 18 000. Fd I ( Ac) will complex iron(II) avidly above pH ∼ 8.0 only when the [3Fe-4S] cluster is reduced and provided that cellular nucleic acid is bound. Fd I ( Ac) rigorously purified from nucleic acid does not undergo iron(II) uptake. These facts, together with recent evidence that the interconversion process [3Fe-4S] 0 + Fe 2+ → [4Fe-4S] 2+ in the iron-responsive element binding protein (IRE-BP) of eukaryotic cells is controlling protein expression at the level of mRNA (1991, Cell 64, 4771; 1991, Nucleic Acid Res. 19, 1739] leads to the following hypothesis. Fd I is a DNA-binding protein which interacts by single α-helix binding in the wide groove of DNA. The binding is regulated by iron(II) levels in the cell. The 7Fe form binds to DNA and represses gene expression. Only the DNA-bound form of the 7Fe Fd I will take up iron(II), not the form free in solution. Iron(II) becomes bound when the [3Fe-4S] cluster is reduced. The 8Fe Fd I thus generated no longer binds DNA and the gene is de-repressed. Sequence comparisons and the crystal structure suggests that the two central turns of the α-helix are important elements of the DNA-recognition process and that residues Gln 69 and Glu 73, which lie on the outer surface of the helix, hydrogen-bond with specific base pairs.