FeoC from Klebsiella pneumoniae uses its iron sulfur cluster to regulate the GTPase activity of the ferrous iron channel

Bacteria depend on the ferrous iron transport (Feo) system for the uptake of ferrous iron (Fe²⁺). The Feo system is crucial for colonization and virulence of pathogens. In γ-proteobacteria, the system consists of FeoA, FeoB, and FeoC. The function of FeoA remains unknown. FeoB likely forms the channel, whose regulation has been suggested to involve its GTPase domain (part of its NFeoB domain). FeoC from Klebsiella pneumonia was found to contain a [4Fe4S] cofactor, whose presence was speculated to enhance the GTPase activity of FeoB (Hsueh, K.-L., et al., J. Bacteriol. 2013 195(20): 4726–34). We present results here that support and extend that hypothesis. We monitored the GTPase activity of FeoB by NMR spectroscopy and found that the presence of 7% FeoC-[4Fe-4S]³⁺ (the highest level of cofactor achieved in vitro) increased the GTPase rate of NFeoB by 3.6-fold over NFeoB. The effect depends on the oxidation state of the cluster; with reduction of the cluster to [4Fe-4S]²⁺ the GTPase greatly decreased the GTPase rate. From the effects of point mutations in FeoC on GTPase rates, we conclude that Lys62 and Lys68 on FeoC each contribute to increased GTPase activity on NFeoB. Mutation of Thr37 of NFeoB to Ser nearly abolished the GTPase activity. The GTPase activity of the isolated K. pneumoniae NFeoB-FeoC complex (NFeoBC) was found to be higher in KCl than in NaCl solution. We solved the X-ray structure of the NFeoBC crystallized from KCl and compared it with a prior X-ray structure crystalized from NaCl. We propose a hypothesis, consistent with these results, to explain the factors that influence the GTPase activity. Bacteria may use the oxygen-sensitive cluster as a sensor to up-regulate the gate closing speed.     

The FeoC Protein Leads to High Cellular Levels of the Fe(II) Transporter FeoB by Preventing FtsH Protease Regulation of FeoB in Salmonella enterica

In the gammaproteobacteria, the FeoA, FeoB, and FeoC proteins constitute the Feo system, which mediates ferrous iron [Fe(II)] import. Of these Feo proteins, FeoB is an inner membrane Fe(II) transporter that is aided by the small protein FeoA. However, the role of another small protein, FeoC, has remained unknown. Here we report that the FeoC protein is necessary for FeoB protein-mediated Fe(II) uptake in Salmonella experiencing low levels of oxygen and iron. The FeoC protein was found to directly bind to the FeoB transporter, leading to high cellular levels of FeoB. Depletion of the FtsH protease enabled high levels of FeoB in the absence of FeoC, suggesting that the FeoC protein protects the FeoB transporter from FtsH-mediated proteolysis. Our present study provides a singular example of bacteria that can control expression of iron uptake systems posttranslationally by employing a small iron transporter-binding protein.     

The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions

In order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe²⁺) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via hydrophobic intercalations into a Leu-rich surface ridge. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate that KpFeoA can assume both “open” and “closed” conformations, controlled by binding at this Leu-rich ridge. We propose a model in which a “C-shaped” clamp along the FeoA surface mediates interactions with its partner protein, FeoB. These findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions and provide a framework for testing FeoA-FeoB interactions, which could be exploited for future antibiotic developments.     

Lon-Mediated Proteolysis of the FeoC Protein Prevents Salmonella enterica from Accumulating the Fe(II) Transporter FeoB under High-Oxygen Conditions

The Salmonella Feo system consists of the FeoA, FeoB, and FeoC proteins and mediates ferrous iron [Fe(II)] import. FeoB is an inner membrane protein that, along with contributions from two small hydrophilic proteins, FeoA and FeoC, transports Fe(II). We previously reported that FeoC binds to and protects the FeoB transporter from FtsH-mediated proteolysis. In the present study, we report proteolytic regulation of FeoC that occurs in an oxygen-dependent fashion. While relatively stable under low-oxygen conditions, FeoC was rapidly degraded by the Lon protease under high-oxygen conditions. The putative Fe-S cluster of FeoC seemed to function as an oxygen sensor to control FeoC stability, as evidenced by the finding that mutation of the putative Fe-S cluster-binding site greatly increased FeoC stability under high-oxygen conditions. Salmonella ectopically expressing the feoB and feoC genes was able to accumulate FeoB and FeoC only under low-oxygen conditions, suggesting that FeoC proteolysis prevents Salmonella from accumulating the FeoB transporter under high-oxygen conditions. Finally, we propose that Lon-mediated FeoC proteolysis followed by FtsH-mediated FeoB proteolysis helps Salmonella to avoid uncontrolled Fe(II) uptake during the radical environmental changes encountered when shifting from low-iron anaerobic conditions to high-iron aerobic conditions.     

FeoC from Klebsiella pneumoniae Contains a [4Fe-4S] Cluster

Iron is essential for pathogen survival, virulence, and colonization. Feo is suggested to function as the ferrous iron (Fe²⁺) transporter. The enterobacterial Feo system is composed of 3 proteins: FeoB is the indispensable component and is a large membrane protein likely to function as a permease; FeoA is a small Src homology 3 (SH3) domain protein that interacts with FeoB; FeoC is a winged-helix protein containing 4 conserved Cys residues in a sequence suitable for harboring a putative iron-sulfur (Fe-S) cluster. The presence of an iron-sulfur cluster on FeoC has never been shown experimentally. We report that under anaerobic conditions, the recombinant Klebsiella pneumoniae FeoC (KpFeoC) exhibited hyperfine-shifted nuclear magnetic resonance (NMR) and a UV-visible (UV-Vis) absorbance spectrum characteristic of a paramagnetic center. The electron paramagnetic resonance (EPR) and extended X-ray absorption fine structure (EXAFS) results were consistent only with the [4Fe-4S] clusters. Substituting the cysteinyl sulfur with oxygen resulted in significantly reduced cluster stability, establishing the roles of these cysteines as the ligands for the Fe-S cluster. When exposed to oxygen, the [4Fe-4S] cluster degraded to [3Fe-4S] and eventually disappeared. We propose that KpFeoC may regulate the function of the Feo transporter through the oxygen- or iron-sensitive coordination of the Fe-S cluster.     

Roles of the Yfe and Feo transporters of Yersinia pestis in iron uptake and intracellular growth

In Yersinia pestis, the Yfe and Feo systems likely function to transport ferrous iron. Both FeoA and FeoB are essential for iron acquisition activity while FeoC is not. Mutations in yfe and feo had an additive effect on microaerophilic growth under iron-chelating conditions. Y. pestis cells lacking the Ybt siderophore-dependent system, the Yfe or the Feo system grow normally in J774A.1 cells. However, a double yfeAB feoB mutant was no longer able to grow in this murine macrophage cell line. This growth defect likely resulted from iron and not manganese deprivation since a yfeAB mntH mutant grew normally in J774A.1 cells. These results suggest that the Yfe and Feo systems are somewhat redundant ferrous iron transporters capable of iron acquisition during intracellular growth of the plague bacterium.     

Structure and Function of the FeoB G-Domain from Methanococcus jannaschii

FeoB in bacteria and archaea is involved in the uptake of ferrous iron (Fe²⁺), an important cofactor in biological electron transfer and catalysis. Unlike any other known prokaryotic membrane protein, FeoB contains a GTP-binding domain at its N-terminus. We determined high-resolution X-ray structures of the FeoB G-domain from Methanococcus jannaschii with and without bound GDP or Mg²⁺-GppNHp. The G-domain forms the same dimer in all three structures, with the nucleotide-binding pockets at the dimer interface, as in the ATP-binding domain of ABC transporters. The G-domain follows the typical fold of nucleotide-binding proteins, with a β-strand inserted in switch I that becomes partially disordered upon GTP binding. Switch II does not contact the nucleotide directly and does not change its conformation in response to the bound nucleotide. Release of the nucleotide causes a rearrangement of loop L6, which we identified as the G5 region of FeoB. Together with the C-terminal helix, this loop may transmit the information about the nucleotide-bound state from the G-domain to the transmembrane region of FeoB.     

Structure of the GTPase and GDI domains of FeoB, the ferrous iron transporter of Legionella pneumophila

Prokaryotic pathogens have developed specialized mechanisms for efficient uptake of ferrous iron (Fe²⁺) from the host. In Legionella pneumophila, the causative agent of Legionnaires’ disease, the transmembrane GTPase FeoB plays a key role in Fe²⁺ acquisition and virulence. FeoB consists of a membrane-embedded core and an N-terminal, cytosolic region (NFeoB). Here, we report the crystal structure of NFeoB from L. pneumophila, revealing a monomeric protein comprising two separate domains with GTPase and guanine-nucleotide dissociation inhibitor (GDI) functions. The GDI domain displays a novel fold, whereas the overall structure of the GTPase domain resembles that of known G domains but is in the rarely observed nucleotide-free state.     

The FeoA protein is necessary for the FeoB transporter to import ferrous iron

In many bacterial feo loci, the feoA gene is associated with the feoB gene. While the feoB-encoded FeoB protein has been demonstrated as a ferrous iron [Fe(II)] transporter, the function of the feoA gene product, FeoA, is unknown. In the present study, we report that the FeoA protein interacts with the FeoB Fe(II) transporter, which is required for FeoB-mediated Fe(II) uptake in Salmonella enterica. Iron uptake assay revealed that in the absence of FeoA, FeoB import of Fe(II) is impaired. Bacterial two-hybrid assay determined that the FeoA protein directly and specifically binds to the FeoB transporter in vivo. This FeoA-FeoB interaction appeared necessary for FeoB-mediated Fe(II) uptake because Salmonella expressing the mutant FeoA that cannot interact with FeoB failed to uptake Fe(II) via the FeoB transporter. Finally, we showed that the FeoA protein does not affect expression of the FeoB transporter per se.     

Structural basis of GDP release and gating in G protein coupled Fe2+ transport

G proteins are key molecular switches in the regulation of membrane protein function and signal transduction. The prokaryotic membrane protein FeoB is involved in G protein coupled Fe²⁺ transport, and is unique in that the G protein is directly tethered to the membrane domain. Here, we report the structure of the soluble domain of FeoB, including the G protein domain, and its assembly into an unexpected trimer. Comparisons between nucleotide free and liganded structures reveal the closed and open state of a central cytoplasmic pore, respectively. In addition, these data provide the first observation of a conformational switch in the nucleotide‐binding G5 motif, defining the structural basis for GDP release. From these results, structural parallels are drawn to eukaryotic G protein coupled membrane processes.     

A Ferrous Iron Exporter Mediates Iron Resistance in Shewanella oneidensis MR-1

Shewanella oneidensis strain MR-1 is a dissimilatory metal-reducing bacterium frequently found in aquatic sediments. In the absence of oxygen, S. oneidensis can respire extracellular, insoluble oxidized metals, such as iron (hydr)oxides, making it intimately involved in environmental metal and nutrient cycling. The reduction of ferric iron (Fe³⁺) results in the production of ferrous iron (Fe²⁺) ions, which remain soluble under certain conditions and are toxic to cells at higher concentrations. We have identified an inner membrane protein in S. oneidensis, encoded by the gene SO_4475 and here called FeoE, which is important for survival during anaerobic iron respiration. FeoE, a member of the cation diffusion facilitator (CDF) protein family, functions to export excess Fe²⁺ from the MR-1 cytoplasm. Mutants lacking feoE exhibit an increased sensitivity to Fe²⁺. The export function of FeoE is specific for Fe²⁺, as an feoE mutant is equally sensitive to other metal ions known to be substrates of other CDF proteins (Cd²⁺, Co²⁺, Cu²⁺, Mn²⁺, Ni²⁺, or Zn²⁺). The substrate specificity of FeoE differs from that of FieF, the Escherichia coli homolog of FeoE, which has been reported to be a Cd²⁺/Zn²⁺ or Fe²⁺/Zn²⁺ exporter. A complemented feoE mutant has an increased growth rate in the presence of excess Fe²⁺ compared to that of the ΔfeoE mutant complemented with fieF. It is possible that FeoE has evolved to become an efficient and specific Fe²⁺ exporter in response to the high levels of iron often present in the types of environmental niches in which Shewanella species can be found.     

The yeast mitochondrial carrier proteins Mrs3p/Mrs4p mediate iron transport across the inner mitochondrial membrane

The yeast proteins Mrs3p and Mrs4p are two closely related members of the mitochondrial carrier family (MCF), which had previously been implicated in mitochondrial Fe²⁺ homeostasis. A vertebrate Mrs3/4 homologue named mitoferrin was shown to be essential for erythroid iron utilization and proposed to function as an essential mitochondrial iron importer. Indirect reporter assays in isolated yeast mitochondria indicated that the Mrs3/4 proteins are involved in mitochondrial Fe²⁺ utilization or transport under iron-limiting conditions. To have a more direct test for Mrs3/4p mediated iron uptake into mitochondria we studied iron (II) transport across yeast inner mitochondrial membrane vesicles (SMPs) using the iron-sensitive fluorophore PhenGreen SK (PGSK). Wild-type SMPs showed rapid uptake of Fe²⁺ which was driven by the external Fe²⁺ concentration and stimulated by acidic pH. SMPs from the double deletion strain mrs3/4Δ failed to show this rapid Fe²⁺ uptake, while SMPs from cells overproducing Mrs3/4p exhibited increased Fe²⁺ uptake rates. Cu²⁺ was transported at similar rates as Fe²⁺, while other divalent cations, such as Zn²⁺ and Cd²⁺ apparently did not serve as substrates for the Mrs3/4p transporters. We conclude that the carrier proteins Mrs3p and Mrs4p transport Fe²⁺ across the inner mitochondrial membrane. Their activity is dependent on the pH gradient and it is stimulated by iron shortage.     

Identification and characterization of zinc-starvation-induced ZIP transporters from barley roots

Zinc (Zn) is an essential element for plants but limited information is currently available on the molecular basis for Zn²⁺ transport in crop species. To expand the knowledge on Zn²⁺ transport in barley (Hordeum vulgare L.), a cDNA library prepared from barley roots was expressed in the yeast (Saccharomyces cerevisiae) mutant strain Δzrt1/Δzrt2, defective in Zn²⁺ uptake. This strategy resulted in isolation and identification of three new Zn²⁺ transporters from barley. All of the predicted proteins have a high similarity to the ZIP protein family, and are designated HvZIP3, HvZIP5 and HvZIP8, respectively. Complementation studies in Δzrt1/Δzrt2 showed restored growth of the yeast cells transformed with the different HvZIPs, although with different efficiency. Transformation into Fe²⁺ and Mn²⁺ uptake defective yeast mutants showed that the HvZIPs were unable to restore the growth on Fe²⁺ and Mn²⁺ limited media, respectively, indicating a specific role in Zn²⁺ transport. In intact barley roots, HvZIP8 was constitutively expressed whereas HvZIP3 and HvZIP5 were mainly expressed in ?Zn plants. These results suggest that HvZIP3, HvZIP5 and HvZIP8 are Zn²⁺ transporters involved in Zn²⁺ homeostasis in barley roots. The new transporters may facilitate breeding of barley genotypes with improved Zn efficiency and Zn content.     

Iron and phosphate uptake explains the calcifuge–calcicole behavior of the terricolous lichens Cladonia furcata subsp. furcata and C. rangiformis

Mechanisms causing the calcifuge–calcicole behavior of lichens are largely unexplored. Studying the case examples of two closely related terricolous lichens, the calcifuge Cladonia furcata subsp. furcata and the calcicole C. rangiformis, we found that preference for acidic or calcareous soils in these lichens is related to iron and phosphate uptake as in vascular plants. In laboratory studies, the calcicole species was more efficient in the intracellular uptake of Fe³⁺ and phosphate at pH 8 than the calcifuge species. At pH 3, intracellular uptake of Fe²⁺ in the calcicole species significantly exceeded that in the calcifuge species suggesting that calcicole lichens suffer from toxicity symptoms by excess Fe²⁺ at acidic sites. Though these observations parallel findings from calcifuge and calcicole vascular plants, mechanisms leading to the different iron and phosphate uptake characteristics in the studied calcifuge and calcicole lichens may differ from those in vascular plants and should be the topic of future research. A role of the depside atranorin in facilitating iron uptake by reducing Fe³⁺ in the apoplast is hypothesized.     

Assessment of iron toxicity using a luminescent bacterial test with an Escherichia coli recombinant strain

The toxic effect of the Fe²⁺ and Fe³⁺ ions on the luminescent recombinant Escherichia coli strain with the luxCDABE operon was studied in short- and long-term experiments. At 30-min exposure of bacteria to the iron ions, the effective concentrations of Fe²⁺ and Fe³⁺ resulting in acute toxicity (EC₅₀) were 8.5 and 1.3 mg/L, respectively. In the long-term (24 h) experiment, during active bacterial growth, the toxicity index for Fe²⁺ and Fe³⁺ was 65.5 and 62.8, respectively. Addition of the iron ions into the medium did not suppress growth, although it inhibited luminescence. Comparative analysis of the short- and long-term experiments made it possible to assess iron toxicity at the concentrations from 0.5 to 20 mg/L (as calculated for the Fe²⁺ and Fe³⁺ ions). Iron ions were found to affect only the reactions that were not vitally important for the cell. At the same time, they had no negative effect on the genetic mechanisms and protein synthesis, thus indicating non-specific toxicity of Fe²⁺ and Fe³⁺.     

Functional reconstitution and characterization of the Arabidopsis Mg2+ transporter AtMRS2-10 in proteoliposomes

Magnesium (Mg²⁺) plays critical role in many physiological processes. The mechanism of Mg²⁺ transport has been well documented in bacteria; however, less is known about Mg²⁺ transporters in eukaryotes. The AtMRS2 family, which consists of 10 Arabidopsis genes, belongs to a eukaryotic subset of the CorA superfamily proteins. Proteins in this superfamily have been identified by a universally conserved GlyMetAsn motif and have been characterized as Mg²⁺ transporters. Some members of the AtMRS2 family, including AtMRS2-10, may complement bacterial mutants or yeast mutants that lack Mg²⁺ transport capabilities. Here, we report the purification and functional reconstitution of AtMRS2-10 into liposomes. AtMRS2-10, which contains an N-terminal His-tag, was expressed in Escherichia coli and solubilized with sarcosyl. The purified AtMRS2-10 protein was reconstituted into liposomes. AtMRS2-10 was inserted into liposomes in a unidirectional orientation. Direct measurement of Mg²⁺ uptake into proteoliposomes revealed that reconstituted AtMRS2-10 transported Mg²⁺ without any accessory proteins. Mutation in the GMN motif, M400 to I, inactivated Mg²⁺ uptake. The AtMRS2-10-mediated Mg²⁺ influx was blocked by Co(III)hexamine, and was independent of the external pH from 5 to 9. The activity of AtMRS2-10 was inhibited by Co²⁺ and Ni²⁺; however, it was not inhibited by Ca²⁺, Fe²⁺, or Fe³⁺. While these results indicate that AtMRS2-10 has similar properties to the bacterial CorA proteins, unlike bacterial CorA proteins, AtMRS2-10 was potently inhibited by Al³⁺. These studies demonstrate the functional capability of the AtMRS2 proteins in proteoliposomes to study structure–function relationships.