Localization of an RNA binding element of the iron responsive element binding protein within a proteolytic fragment containing iron coordination ligands

Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA

Iron regulatory protein 1 (IRP1) binds iron-responsive elements (IREs) in messenger RNAs (mRNAs), to repress translation or degradation, or binds an iron-sulfur cluster, to become a cytosolic aconitase enzyme. The 2.8 angstrom resolution crystal structure of the IRP1:ferritin H IRE complex shows an open protein conformation compared with that of cytosolic aconitase. The extended, L-shaped IRP1 molecule embraces the IRE stem-loop through interactions at two sites separated by approximately 30 angstroms, each involving about a dozen protein:RNA bonds. Extensive conformational changes related to binding the IRE or an iron-sulfur cluster explain the alternate functions of IRP1 as an mRNA regulator or enzyme.

Crystallization and preliminary X-ray diffraction analysis of iron regulatory protein 1 in complex with ferritin IRE RNA

Iron regulatory protein 1 (IRP1) is a bifunctional protein with activity as an RNA-binding protein or as a cytoplasmic aconitase. Interconversion of IRP1 between these mutually exclusive states is central to cellular iron regulation and is accomplished through iron-responsive assembly and disassembly of a [4Fe-4S] cluster. When in its apo form, IRP1 binds to iron responsive elements (IREs) found in mRNAs encoding proteins of iron storage and transport and either prevents translation or degradation of the bound mRNA. Excess cellular iron stimulates the assembly of a [4Fe-4S] cluster in IRP1, inhibiting its IRE-binding ability and converting it to an aconitase. The three-dimensional structure of IRP1 in its different active forms will provide details of the interconversion process and clarify the selective recognition of mRNA, Fe-S sites and catalytic activity. To this end, the apo form of IRP1 bound to a ferritin IRE was crystallized. Crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 109.6, b = 80.9, c = 142.9 A, beta = 92.0 degrees. Native data sets have been collected from several crystals with resolution extending to 2.8 A and the structure has been solved by molecular replacement.

A Northwestern blotting approach for studying iron regulatory element-binding proteins

At least two proteins binding to iron regulatory elements (IRE) in mRNA are known, designated as iron regulatory proteins (IRP) 1 and 2. Their binding activity is widely studied by electrophoretic mobility shift assays (EMSA), which resolves one or two bands depending on the species. We used Northwestern blotting to resolve this EMSA complex into four components, and identified two other IRE-binding peptides present in HepG2 cell extracts. We designate these six peptide bands A to F on Northwestern blots, ranging in apparent molecular weight from 111 to 37 kDa. Band C is lost when cells are preloaded with iron or when leupeptin (but not several other protease inhibitors) is included in the extraction buffer. Band E is also lost with leupeptin but increases with iron loading. Binding of all bands is sensitive to iron in vitro. Two-dimensional electrophoresis reveals additional processing, especially indicating charge variants of band C. Northwestern bands A and B both react with an antibody to IRP-1 on parallel Western blots. We conclude that cellular processing can produce multiple IRE-binding species that may be involved in a more complex regulation of iron metabolism than generally appreciated. The Northwestern approach should facilitate studies of processing and binding requirements of proteins and peptides that recognize the IRE sequence.

Endogenous nitration of iron regulatory protein-1 (IRP-1) in nitric oxide-producing murine macrophages: further insight into the mechanism of nitration in vivo and its impact on IRP-1 functions

Iron regulatory protein-1 (IRP-1) is a bifunctional [4Fe-4S] protein that functions as a cytosolic aconitase or as a trans-regulatory factor controlling iron homeostasis at a post-transcriptional level. Because IRP-1 is a sensitive target protein for nitric oxide (NO), we investigated whether this protein is nitrated in inflammatory macrophages and whether this post-transcriptional modification changes its activities. RAW 264.7 macrophages were first stimulated with interferon-gamma and lipopolysaccharide (IFN-gamma/LPS) and then triggered by phorbol 12-myristate 13-acetate (PMA) in order to promote co-generation of NO* and O*2-.. IRP-1 was isolated by immunoprecipitation and analyzed for protein-bound nitrotyrosine by Western blotting. We show that nitration of endogenous IRP-1 in NO-producing macrophages boosted to produce O*2- was accompanied by aconitase inhibition and impairment of its capacity to bind the iron-responsive element (IRE) of ferritin mRNA. Lost IRE-binding activity was not recovered by exposure of IRP-1 to 2% 2-mercaptoethanol and was not due to protein degradation. Inclusion of cis-aconitate with cell extract to stabilize the [4Fe-4S] cluster of holo-IRP-1 rendered protein insensitive to nitration by peroxynitrite, suggesting that loss of [Fe-S] cluster and subsequent change of conformation are prerequisites for tyrosine nitration. IRP-1 nitration was strongly reduced when IFN-gamma/LPS/PMA-stimulated cells were incubated with myeloperoxidase inhibitors, which points to the contribution of the nitrite/H2O2/peroxidase pathway to IRP-1 nitration in vivo. Interestingly, under these conditions, IRP-1 recovered full IRE binding as assessed by treatment with 2% 2-mercaptoethanol. Peroxidase-mediated nitration of critical tyrosine residues, by holding IRP-1 in an inactive state, may constitute, in activated macrophages, a self-protecting mechanism against iron-induced toxicity.

A high-capacity RNA affinity column for the purification of human IRP1 and IRP2 overexpressed in Pichia pastoris

Regulated expression of proteins involved in mammalian iron metabolism is achieved in part through the interaction of the iron regulatory proteins IRP1 and IRP2 with highly conserved RNA stem-loop structures, known as iron-responsive elements (IREs), that are located within the 5' or 3' untranslated regions of regulated transcripts. As part of an effort to determine the structures of the IRP-IRE complexes using crystallographic methods, we have developed an efficient process for obtaining functionally pure IRP1 and IRP2 that relies upon the improved overexpression (>10 mg of soluble IRP per liter of culture) of each human IRP in the yeast Pichia pastoris and large-scale purification using RNA affinity chromatography. Despite the utility of RNA affinity chromatography in the isolation of RNA-binding proteins, current methods for preparing RNA affinity matrices produce columns of low capacity and limited stability. To address these limitations, we have devised a simple method for preparing stable, reusable, high-capacity RNA affinity columns. This method utilizes a bifunctional linker to covalently join a 5'-amino tethered RNA with a thiol-modified Sepharose, and can be used to load 150 nmole or more of RNA per milliliter of solid support. We demonstrate here the use of an IRE affinity column in the large-scale purification of IRP1 and IRP2, and suggest that the convenience of this approach will prove attractive in the analysis of other RNA-binding proteins.

Manduca sexta IRP1: molecular characterization and in vivo response to iron

Manduca sexta IRP1 was cloned and sequenced. The deduced amino acid sequence of Manduca IRP1 shows high similarity to other IRP1 proteins. The Cys residues required as ligands for the iron sulfur cluster, as well as all residues necessary for aconitase activity are conserved in the insect protein. Purified recombinant Manduca IRP1 binds specifically to transcripts of the iron responsive element (IRE) of Manduca or human ferritin subunit mRNA. Binding activity of the recombinant protein was not influenced by the presence of beta-mercaptoethanol. However, IRP/IRE binding activity of cytoplasmic extracts from fat body was decreased by reducing agents in a dose-responsive manner. Fat body IRP1/IRE binding activity was reduced for Manduca sexta larvae injected with low doses of iron, while IRP1 mRNA and protein levels remained stable. At higher iron doses, binding activity increased and stabilized. Hemolymph ferritin levels showed an inverse relationship to IRP1/IRE binding activity. These data suggest that the Manduca IRP1 is likely involved in translational control of ferritin synthesis in a manner similar to that found in vertebrates. However, factors other than iron can influence IRP/IRE interaction and hemolymph ferritin levels in insects.

Regulation of genes of iron metabolism by the iron-response proteins

Iron is an essential nutrient, yet excess iron can be toxic to cells. The uptake of iron by mammalian cells is post-transcriptionally regulated by the interaction of iron-response proteins (IRP1 and IRP2) with iron-response elements (IREs) found in the mRNAs of genes of iron metabolism, such as ferritin, the transferrin receptor, erythroid aminolevulinic acid synthase, and mitochondrial aconitase. The IRPs are RNA binding proteins that bind to the IRE (found in the mRNAs of the regulated genes) in an iron- dependent manner. Binding of IRPs to the IREs leads to changes in the expression of the regulated genes and subsequent changes in the uptake, utilization, or storage of intracellular iron. Recent work has demonstrated that the binding of the IRPs to the IREs can also be modulated by changes in the redox state or oxidative stress level of the cell. These findings provide an important link between iron metabolism and states of oxidative stress.

Ligand-induced structural alterations in human iron regulatory protein-1 revealed by protein footprinting

Human iron regulatory protein-1 (IRP-1) is a bifunctional protein that regulates iron metabolism by binding to mRNAs encoding proteins involved in iron uptake, storage, and utilization. Intracellular iron accumulation regulates IRP-1 function by promoting the assembly of an iron-sulfur cluster, conferring aconitase activity to IRP-1, and hindering RNA binding. Using protein footprinting, we have studied the structure of the two functional forms of IRP-1 and have mapped the surface of the iron-responsive element (IRE) binding site. Binding of the ferritin IRE or of the minimal regulatory region of transferrin receptor mRNA induced strong protections against proteolysis in the region spanning amino acids 80 to 187, which are located in the putative cleft thought to be involved in RNA binding. In addition, IRE-induced protections were also found in the C-terminal domain at Arg-721 and Arg-728. These data implicate a bipartite IRE binding site located in the putative cleft of IRP-1. The aconitase form of IRP-1 adopts a more compact structure because strong reductions of cleavage were detected in two defined areas encompassing residues 149 to 187 and 721 to 735. Thus both ligands of apo-IRP-1, the IRE and the 4Fe-4S cluster, induce distinct but overlapping alterations in protease accessibility. These data provide evidences for structural changes in IRP-1 upon cluster formation that affect the accessibility of residues constituting the RNA binding site.

Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins

The iron responsive element (IRE) is a approximately 30 nucleotide RNA hairpin that is located in the 5' untranslated region of all ferritin mRNAs and in the 3' untranslated region of all transferrin receptor mRNAs. The IREs are bound by two related IRE-binding proteins (IRPs) which help control intracellular levels of iron by regulating the expression of both ferritin and transferrin receptor genes. Multi-dimensional NMR and computational approaches were used to study the structure and dynamics of the IRE RNA in solution. The NMR data are consistent with formation of A-form helical stem regions, a one-base internal bulge and a Watson-Crick C.G base-pair between the first and fifth nucleotides in the loop. A superposition of refined structures indicates that the conserved C in the internal bulge, and three residues in the six-nucleotide hairpin loop are quite dynamic in this RNA. The structural roles of the stems, the loop and the bulge in the function of the IRE RNA and in possible interactions with the iron regulatory protein are discussed.

Redox modulation of iron regulatory proteins by peroxynitrite

Expression of several proteins of higher eukaryotes is post-transcriptionally regulated by interaction of iron-responsive elements (IREs) on their mRNAs and iron regulatory proteins (IRP1 and IRP2). IRP1 is a redox-sensitive iron-sulfur protein whose regulatory activity is modulated by iron depletion, synthesis of nitric oxide, or oxidative stress. IRP2 is closely related to IRP1, but it does not possess a [Fe-S] cluster. IRP2 is also regulated by intracellular iron level, but it is assumed that regulation is achieved by accelerated turn-over. In this report, the effect of peroxynitrite, a strong oxidant produced when nitric oxide and O-2 are biosynthesized simultaneously, on the RNA binding activity of IRP1 and IRP2 was investigated in vitro. Macrophage cytosolic extracts were exposed directly to a bolus addition of peroxynitrite or to SIN-1, which releases a continuous flux of peroxynitrite. Under these two experimental conditions, IRP1 lost its aconitase activity but did not gain increased capacity to bind IRE. However, addition of low amounts of the disulfide-reducing agent 2-ME during the binding assay revealed formation of a complex between IRP1 and IRE. Substrates of aconitase, which bind to the cluster of IRP1, prevented this effect, pointing to the [Fe-S] cluster as the target of peroxynitrite. Moreover, single mutation of the redox active Cys437 precluded oxidation of human recombinant IRP1 by SIN-1. Collectively, these results imply that peroxynitrite predisposes IRP1 to bind IREs under a suitable reducing environment. It is assumed that in addition to disrupting the cluster peroxynitrite also promotes disulfide bridge(s) between proximal cysteine residues in the vicinity of the IRE-binding domain, in particular Cys437. When exposed to peroxynitrite, IRP2 lost its spontaneous IRE binding activity, which was restored by further exposure to 2-mercaptoethanol, thus showing that peroxynitrite can also regulate IRP2 by a post-translational event.

Interplay between NO and [Fe-S] clusters: relevance to biological systems

In mammalian cells, nitric oxide (NO) synthesis results in the inactivation of several mitochondrial iron-sulfur enzymes involved in ATP synthesis that correlates with the appearance of complexes of the [(NO)2Fe(SR)2] type detectable by electron paramagnetic resonance spectroscopy. More specifically, the activity of two [Fe-S] enzymes was followed during the course of NO synthase expression:mitochondrial aconitase, which catalyzes citrate:isocitrate conversion in the Krebs cycle, and cytoplasmic aconitase, or iron regulatory protein (IRP), a trans-regulator that controls expression at the posttranscriptional level of proteins involved in iron metabolism. In response to physiological stimuli, the synthesis of NO leads to inhibition of enzymatic activities of both mitochondrial and cytoplasmic aconitases, whereas the RNA binding activity of IRP is increased. Coordination of the diffusible gas NO with [Fe-S] clusters is thought to result in impairment of metabolic functions. Here it is proposed that the interplay between NO (or some NO-derived molecule) and [Fe-S] clusters at critical catalytic or allosteric sites is crucial in the response to environmental signals within cells.

Interaction between iron-regulatory proteins and their RNA target sequences, iron-responsive elements

In this chapter, we have focused on the biochemistry of IRP-1 and the features which distinguish it from the related RNA-binding protein, IRP-2. IRP-1 is the cytoplasmic isoform of the enzyme aconitase, and, depending on iron status, may switch between enzymatic and RNA-binding activities. IRP-1 and IRP-2 are trans-acting regulators of mRNAs involved in iron uptake, storage and utilisation. The finding of an IRE in the citric acid cycle enzymes, mitochondrial aconitase and succinate dehydrogenase, suggests that the IRPs may also influence cellular energy production. These two proteins appear to bind RNAs with different but overlapping specificity, suggesting that they may regulate the stability or translation of as yet undefined mRNA targets, possibly extending their regulatory function beyond that of iron homeostasis. The interaction between the IRPs and the IRE represents one of the best characterised model systems for posttranscriptional gene control, and given that each IRP can also recognise its own unique set of RNAs, the search for new in vivo mRNA targets is expected to provide yet more surprises and insights into the fate of cytoplasmic mRNAs.

Regulation of iron metabolism in eukaryotes

Iron metabolism is regulated in cells to ensure that iron supplies are adequate and nontoxic. The expression of iron metabolism is regulated primarily by posttranscriptional mechanisms. Ferritin, eALAS, SDHb of Drosophila, and mammalian mitochondrial aconitase are translationally regulated. The TfR is regulated at the level of mRNA stability. Iron regulatory proteins are regulated either by assembly or by disassembly of an iron-sulfur cluster (IRP1) or by rapid degradation in the presence of iron (IRP2). The list of targets for IRP-mediated regulation is growing longer, and a range of possibilities for versatile regulation exists, as each IRP can bind to unique targets that differ from the consensus IRE. The reactivity of iron with oxygen and the creation of toxic by-products may be the evolutionary stimulus that produced this system of tight posttranscriptional gene regulation.

Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress

As an essential nutrient and a potential toxin, iron poses an exquisite regulatory problem in biology and medicine. At the cellular level, the basic molecular framework for the regulation of iron uptake, storage, and utilization has been defined. Two cytoplasmic RNA-binding proteins, iron-regulatory protein-1 (IRP-1) and IRP-2, respond to changes in cellular iron availability and coordinate the expression of mRNAs that harbor IRP-binding sites, iron-responsive elements (IREs). Nitric oxide (NO) and oxidative stress in the form of H2O2 also signal to IRPs and thereby influence cellular iron metabolism. The recent discovery of two IRE-regulated mRNAs encoding enzymes of the mitochondrial citric acid cycle may represent the beginnings of elucidating regulatory coupling between iron and energy metabolism. In addition to providing insights into the regulation of iron metabolism and its connections with other cellular pathways, the IRE/IRP system has emerged as a prime example for the understanding of translational regulation and mRNA stability control. Finally, IRP-1 has highlighted an unexpected role for iron sulfur clusters as post-translational regulatory switches.

Modulation by nitric oxide of metalloprotein regulatory activities

In many cells, a nitric oxide (NO) synthase inducible by immunological stimuli produces a sustained flow of NO that lasts a long time. NO is a short-lived molecule but it is a diffusible ligand believed to be capable of reaching distal target sites. Further, several lines of evidence indicate that cysteine-rich motifs of metal-binding proteins, as well as redox-sensitive metal clusters of metalloproteins, are natural sensors of bioradicals like NO. In metalloregulatory proteins, metals are often conveniently located at binding sites and bound to cysteine residues. Accordingly, disruption of the metal-thiolate polymetallic clusters should trigger significant remodelling of the protein structure involved in regulation. We can therefore postulate that the nitrosation reaction occurring at metal centres or cysteine-rich motifs will preclude correct binding to regulatory sites. Several examples are given of metalloregulatory proteins whose metal is bound to thiols and may then become sensitive to NO. Recent observations indicate that in response to NO synthesis, iron regulatory protein, a eukaryotic bifunctional [Fe-S] protein, switches from acting as aconitase to being an RNA-binding regulator, and we suggest that the interplay between NO or a NO-derived molecule and metal clusters at critical allosteric sites may be a crucial component of the cellular response to environmental stress.

Modulation of iron regulatory protein functions. Further insights into the role of nitrogen- and oxygen-derived reactive species

Iron regulatory protein (IRP) is a cytosolic bifunctional [Fe-S] protein which exhibits aconitase activity or binds iron responsive elements (IREs) in untranslated regions of specific mRNA. The modulators of these activities are the intracellular concentration of iron and, as recently described, NO synthase activity. In this study, we attempted to establish in in vitro experiments whether peroxynitrite (ONOO-, the product of the reaction between NO and O2-.), as well as oxygen-derived radicals (O2-. and H2O2) and various NO donors, allow IRP to bind IREs using cytosol extract of macrophagelike RAW 264.7 cells. Neither the addition of a bolus of ONOO- or H2O2 nor O2-. generation significantly affected IRE binding even though they inhibited its aconitase activity. Moreover, we show that 3-morpholinosydnonimine (SIN-1), a chemical which releases both NO and O2-. enhanced IRE binding activity of IRP only in the presence of superoxide dismutase (SOD). S-Nitrosothiols and the NONOate sper/NO plus gluthathione (GSH) activated IRE binding by IRP whereas oxyhemoglobin prevented enhancement of this binding by SIN-1/SOD and sper/NO plus GSH. cis-Aconitate, substrate, also abolished the effect of SIN-1/SOD on IRE binding by IRP. These results imply that neither O2-. nor ONOO- can convert [4Fe-4S] IRP into IRE-binding protein but rather suggest that an active redox form of NO converts IRP into its IRE binding form by targeting the [Fe-S] cluster.

Iron regulates the intracellular degradation of iron regulatory protein 2 by the proteasome

Iron regulatory proteins (IRP1 and IRP2) are RNA-binding proteins that bind to specific structures, termed iron-responsive elements (IREs), that are located in the 5'- or 3'-untranslated regions of mRNAs that encode proteins involved in iron homeostasis. IRP1 and IRP2 RNA binding activities are regulated by iron; IRP1 and IRP2 bind IREs with high affinity in iron-depleted cells and with low affinity in iron-repleted cells. The decrease in IRP1 RNA binding activity occurs by a switch between apoprotein and 4Fe-4S forms, without changes in IRP1 levels, whereas the decrease in IRP2 RNA binding activity reflects a reduction in IRP2 levels. To determine the mechanism by which iron decreases IRP2 levels, we studied IRP2 regulation by iron in rat hepatoma and human HeLa cells. The iron-dependent decrease in IRP2 levels was not due to a decrease in the amount of IRP2 mRNA or to a decrease in the rate of IRP2 synthesis. Pulse-chase experiments demonstrated that iron resulted in a 3-fold increase in the degradation rate of IRP2. IRP2 degradation depends on protein synthesis, but not transcription, suggesting a requirement for a labile protein. IRP2 degradation is not prevented by lysosomal inhibitors or calpain II inhibitors, but is prevented by inhibitors that block proteasome function. These data suggest the involvement of the proteasome in iron-mediated IRP2 proteolysis.

A novel method to identify nucleic acid binding sites in proteins by scanning mutagenesis: application to iron regulatory protein

We describe a new procedure to identify RNA or DNA binding sites in proteins, based on a combination of UV cross-linking and single-hit chemical peptide cleavage. Site-directed mutagenesis is used to create a series of mutants with single Asn-Gly sequences in the protein to be analysed. Recombinant mutant proteins are incubated with their radiolabelled target sequence and UV irradiated. Covalently linked RNA- or DNA-protein complexes are digested with hydroxylamine and labelled peptides identified by SDS-PAGE and autoradiography. The analysis requires only small amounts of protein and is achieved within a relatively short time. Using this method we mapped the site at which human iron regulatory protein (IRP) is UV cross-linked to iron responsive element RNA to amino acid residues 116-151.