Iron increases synthesis rates of proteins encoded in iron-responsive element (IRE)-mRNAs; metabolic iron ("free," "labile") is Fe 2þ . The noncoding IRE-RNA structure, approximately 30 nt, folds into a stem loop to control synthesis of proteins in iron trafficking, cell cycling, and nervous system function. IRE-RNA riboregulators bind specifically to iron-regulatory proteins (IRP) proteins, inhibiting ribosome binding. Deletion of the IRE-RNA from an mRNA decreases both IRP binding and IRP-independent protein synthesis, indicating effects of other "factors." Current models of IRE-mRNA regulation, emphasizing iron-dependent degradation/modification of IRP, lack answers about how iron increases IRE-RNA/IRP protein dissociation or how IRE-RNA, after IRP dissociation, influences protein synthesis rates. However, we observed Fe 2þ (anaerobic) or Mn 2þ selectively increase the IRE-RNA/IRP K D . Here we show: (i) Fe 2þ binds to the IRE-RNA, altering its conformation (by 2-aminopurine fluorescence and ethidium bromide displacement); (ii) metal ions increase translation of IRE-mRNA in vitro; (iii) eukaryotic initiation factor (eIF)4F binds specifically with high affinity to IRE-RNA; (iv) Fe 2þ increased eIF4F/IRE-RNA binding, which outcompetes IRP binding; (v) exogenous eIF4F rescued metal-dependent IRE-RNA translation in eIF4F-depeleted extracts. The regulation by metabolic iron binding to IRE-RNA to decrease inhibitor protein (IRP) binding and increase activator protein (eIF4F) binding identifies IRE-RNA as a riboregulator.ferrous ion regulation | metabolic riboregulator I ron increases rates of ferritin protein synthesis in animals by facilitating messenger RNA/ribosome binding; metabolic iron (i.e., "labile" or "free" iron in cells) is considered to be ferrous (1). The iron response requires a noncoding riboregulator called the "iron-responsive element" (IRE), which is approximately 30 nt, folded into a distorted, bulged helix loop (2-5). This riboregulatory structure is also found in mRNAs for proteins of iron traffic (6-9), cell cycling (10), and the nervous system (11). IRP proteins bind with different stabilities to IRE-RNAs of the IRE-RNA family (12, 13), creating a graded or hierarchal set of mRNA responses to iron in vivo. Deletion of the 30 nt IRE-RNA not only removes IRP regulation but also decreases the rate of IRP-independent protein synthesis (14). A number of current models of IRE-RNA/IRP regulation feature iron-dependent degradation/modification of the IRP proteins as the main control point (8,9,15,16). Such models do not answer two important questions: (i) How does iron increase release of IRP protein for [4Fe-4S]-modification and/or degradation? Overlap of the IRE-RNA and the Fe-S binding sites on IRP1 prevents Fe-S insertion in the IRP1/IRE-RNA complex (5). (ii) How does the IRE-RNA control rates of IRP-independent protein synthesis (14)? In an earlier study, we showed that Fe 2þ ions (anaerobic) selectively increased the dissociation constant for the IRE-RNA/IRP1 complex in solution (12). Here we r...

Ferritins are an ancient superfamily of protein nanocages that synthesize, reversibly, iron concentrates for cellular use, heme, FeS cluster, and Fe-protein synthesis and provide oxidant protection by consumption of dioxygen or hydrogen peroxide and ferrous iron during stress; the protein cavities containing the minerals are ϳ60% of the cage volume (1-4). Ferritins differ in cage size, location, and mechanism of catalytic sites, mineral size, and mineral crystallinity; the Fe 2ϩ /O 2 oxidoreductase sites are also called ferroxidase sites or FC (ferroxidase centers) sites (1-5). In eukaryotic H ferritins, Fe 2ϩ and dioxygen are substrates for oxidoreductase sites and are catalytically coupled at multiple protein sites to synthesize diferric oxo mineral precursors (Fig. 1). Consumption of both iron and oxygen by ferritins accounts for the antioxidant response and iron-controlled gene regulation of ferritins in eukaryotes (6). Many catalytic proteins use iron and oxygen to produce a variety of organic products. Such products include unsaturated fatty acids such as oleate stearoyl-CoA desaturase-1 (7), deoxyribose (ribonucleotide reductase), and prolyhydroxyl modification of oxygen-sensing DNA transcription factors, e.g. hypoxia-inducible factor-␣ (8). Only in ferritins are both substrates inorganic. The exclusive use of inorganic substrates may relate to the ancient origins of the ferritins, which are distributed in all kingdoms and in both anaerobes and aerobes; ferritin gene deletion is lethal early in mammalian embryogenesis (9).There are two types of protein channels that move iron into and through the 24 subunit cages during synthesis of [Fe 3ϩ O] n in eukaryotic ferritins. The two functional types of ferritin channels are: (i) ion entry channels around the 3-fold axes, for , where diferric oxo mineral precursors produced by oxidoreduction fuse to tetramers and larger multimers before exiting from the protein cage for mineral growth.Recent high resolution structural studies show that ferritin is a soluble ion channel protein with lines of multiple metal ions (10), much like K ϩ and other membrane ion channel proteins. The eight Fe 2ϩ entry channels (Fig. 1) suggest roles beyond just electrostatics for the conserved carboxylates, such as ion selectivity at the channel constriction or directing Fe 2ϩ substrate ions to active sites in three subunits that also form the entry channels (10). The Fe 3ϩ O nucleation channels were recently identified using 13 C-13 C solution NMR spectroscopy in the presence and absence of Fe 3ϩ , by the disappearance of resonances within 5 Å of Fe 3ϩ O moving away from the active sites (11). Nucleation channel exits into the cavity are clustered around the 4-fold axes of the cage, which facilitates ordered mineral growth. 4 The abbreviations used are: DFP, diferric peroxo; MCD, magnetic circular dichroism; bis-Tris, bis(2-hydroxyethyl)iminotris(hydroxymethyl)methane.

We have engineered a pathway for the formation of disulfide bonds. By imposing evolutionary pressure, we isolated mutations that changed thioredoxin, which is a monomeric disulfide reductase, into a [2Fe-2S] bridged dimer capable of catalyzing O2-dependent sulfhydryl oxidation in vitro. Expression of the mutant protein in Escherichia coli with oxidizing cytoplasm and secretion via the Tat pathway restored disulfide bond formation in strains that lacked the complete periplasmic oxidative machinery (DsbA and DsbB). The evolution of [2Fe-2S] thioredoxin illustrates how mutations within an existing scaffold can add a cofactor and markedly change protein function.

Ferritin has a binuclear non-heme iron active site that functions to oxidize iron as a substrate for formation of an iron mineral core. Other enzymes of this class have tightly bound diiron cofactor sites that activate O2 to react with substrate. Ferritin has an active site ligand set with 1-His/4-carboxylate/1-Gln rather than the 2-His/4-carboxylate set of the cofactor site. This ligand variation has been thought to make a major contribution to this biferrous substrate rather than cofactor site reactivity. However, the Q137E/D140H double variant of M ferritin, has a ligand set that is equivalent to most of the diiron cofactor sites, yet did not rapidly react with O2 or generate the peroxy intermediate observed in the cofactor sites. Therefore, in this study, a combined spectroscopic methodology of circular dichroism (CD)/magnetic CD (MCD)/variable temperature, variable field (VTVH) MCD has been applied to evaluate the factors required for the rapid O2 activation observed in cofactor sites. This methodology defines the coordination environment of each iron and the bridging ligation of the biferrous active sites in the double and corresponding single variants of frog M ferritin. Based on spectral changes, the D140H single variant has the new His ligand binding, and the Q137E variant has the new carboxylate forming a μ-1,3 bridge. The spectra for the Q137E/D140H double variant, which has the cofactor ligand set, however, reflects a site that is more coordinately saturated than the cofactor sites in other enzymes including ribonucleotide reductase, indicating the presence of additional water ligation. Correlation of this double variant and the cofactor sites to their O2 reactivities indicates that electrostatic and steric changes in the active site and, in particular, the hydrophobic nature of a cofactor site associated with its second sphere protein environment, make important contributions to the activation of O2 by the binuclear non-heme iron enzymes.