Electron spin resonance study of rapidly frozen solution of iron-glutathione

Rapidly mixed anaerobic solutions (at pH 2.7) of FeCl₃ and glutathione were quickly frozen at various times after mixing. EPR spectra of these frozen solutions showed the progressive reduction of the iron(III) with time and the transient presence of a g = 2 radical signal. This signal is discussed in terms of an intermediate in the reduction pathway containing a high spin iron(II) centre weakly coupled to a sulphur radicalSimilar experiments were carried out at pH 9 in the presence of oxygen.     

Physiological and transcriptional responses in the iron–sulphur cluster assembly pathway under abiotic stress in peach (Prunus persica L.) seedlings

As one of the most indispensable element in mineral nutrition of plants, iron (Fe) is closely related to fruits quality and yield. However, molecular mechanisms towards Fe metabolism in fruit trees is largely unclear. In higher plants, iron–sulphur (Fe–S) cluster assembly occurs in chloroplasts, mitochondria and cytosol involving dozens of genes. In this study, we identified 44 putative Fe–S cluster assembly genes in peach (Prunus persica cv. ‘Xiahui6’), and analyzed Fe–S cluster assembly gene expression profiles in response to abiotic stresses. Peach seedlings were more sensitive to iron deficiency, drought and salinity stress, evidenced in reduced photosynthetic performance and altered activity of nitrite reductase, succinate dehydrogenase and aconitase. In addition, Fe–S cluster assembly genes are differentially regulated by abiotic stresses. Iron depletion and drought stress are likely to affect Fe–S cluster assembly genes in leaves. Excess iron toxicity mainly induces Fe–S cluster assembly gene expression in roots, whereas salinity stress massively inhibits Fe–S cluster assembly gene expression in roots. Interestingly, we found that un-functional scaffolds are more prone to disappear during the long-term evolution in perennial woody plants. Our findings directly provide molecular basis for Fe metabolism in peach, and favorably reveal potential candidate genes for further functional determination.     

A combined computational and experimental investigation of the [2Fe–2S] cluster in biotin synthase

Biotin synthase was the first example of what is now regarded as a distinctive enzyme class within the radical S-adenosylmethionine superfamily, the members of which use Fe/S clusters as the sulphur source in radical sulphur insertion reactions. The crystal structure showed that this enzyme contains a [2Fe–2S] cluster with a highly unusual arginine ligand, besides three normal cysteine ligands. However, the crystal structure is at such a low resolution that neither the exact coordination mode nor the role of this exceptional ligand has been elucidated yet, although it has been shown that it is not essential for enzyme activity. We have used quantum refinement of the crystal structure and combined quantum mechanical and molecular mechanical calculations to explore possible coordination modes and their influences on cluster properties. The investigations show that the protonation state of the arginine ligand has little influence on cluster geometry, so even a positively charged guanidinium moiety would be in close proximity to the iron atom. Nevertheless, the crystallised enzyme most probably contains a deprotonated (neutral) arginine coordinating via the NH group. Furthermore, the Fe···Fe distance seems to be independent of the coordination mode and is in perfect agreement with distances in other structurally characterised [2Fe–2S] clusters. The exceptionally large Fe···Fe distance found in the crystal structure could not be reproduced.     

Controlled Diet in Phenylketonuria and Hyperphenylalaninemia may Cause Serum Selenium Deficiency in Adult Patients: The Czech Experience

Phenylketonuria is an inherited disorder of metabolism of the amino acid phenylalanine caused by a deficit of the enzyme phenylalanine hydroxylase. It is treated with a low-protein diet containing a low content of phenylalanine to prevent mental affection of the patient. Because of the restricted intake of high-biologic-value protein, patients with phenylketonuria may have lower than normal serum concentrations of pre-albumin, selenium, zinc and iron. The objective of the present study was to assess the compliance of our phenylketonuric (PKU) and hyperphenylalaninemic (HPA) patients; to determine the concentration of serum pre-albumin, selenium, zinc and iron to discover the potential correlation between the amount of proteins in food and their metabolic control. We studied 174 patients of which 113 were children (age 1–18), 60 with PKU and 53 with HPA and 61 were adults (age 18–42), 51 with PKU and 10 with HPA. We did not prove a statistically significant difference in the concentration of serum pre-albumin, zinc and iron among the respective groups. We proved statistically significant difference in serum selenium concentrations of adult PKU and HPA patients (p?=?0.006; Mann–Whitney U test). These results suggest that controlled low-protein diet in phenylketonuria and hyperphenylalaninemia may cause serum selenium deficiency in adult patients.     

Activity of enzymes involved in lignin biosynthesis in swede root disks

The activity of nine enzymes involved in the biosynthesis of lignin precursors has been studied during the ageing of swede root disks in the presence and absence of ethylene. Peroxidase, aromatic alcohol dehydrogenase and phenylalanine transaminase show very little change in activity during ageing under either ageing condition. O-methyl transferase, shikimate dehydrogenase and ferulyl CoA reductase show only a 2–3 fold increase on ageing and are relatively insensitive to ethylene treatment. A third group (comprising phenylalanine ammonia lyase, cinnamic acid-4-hydroxylase and hydroxycinnamate CoA ligase) show 20–30 fold increase on ageing and are most sensitive to ethylene treatment. Phenylalanine ammonia lyase and cinnamic acid-4-hydroxylase behave very similarly in respect of their time course of ageing and in their responses to metabolic inhibitors such as cycloheximide, puromycin and actinomycin D. In addition the properties of the O-methyl transferase of swede root tissue are described.     

Heterogeneity of rabbit platelets. Effect of chronic blood loss on glycolytic and related enzyme activity

Rabbits were chronically bled, with Fe replacement, every 3–4 days for 21 days. Their platelet count and megathrombocyte number (large-heavy, young platelets) increased 1.7-and 2.3-fold, respectively. Eight of the 11 enzymes of the Embden-Meyerhof pathway increased 2–5-fold in activity per g wet weight during the period of blood letting. The five related enzymes (phosphoglucomutase, glucose 6-P dehydrogenase, 6-P gluconic dehydrogenase, glutathione reductase, and α-glycerol-P dehydrogenase) as well as the three Embden-Meyerhof pathway enzymes (aldolase, enolase, and pyruvate kinase) did not increase in activity over basal values. It is concluded that chronic blood loss with Fe replacement leads to a specific increase in enzyme activity of 8 of the 11 Embden-Meyerhof pathway enzymes.     

Simplified isolation and molecular composition of NADH dehydrogenase of the respiratory chain.

A simplified procedure for the isolation of NADH dehydrogenase from the inner membrane of ox heart mitochondria is presented which permits relatively rapid preparation of the enzyme in a more stable form than that afforded by published methods. The protein thus isolated displays more than eight different subunits in gel electrophoresis under denaturing conditions, three of which are also present in the "low-molecular-weight form' of the enzyme prepared under more drastic conditions. Complex I contains several subunits, mostly of low molecular weight, not seen in soluble purified NADH dehydrogenase. It is suggested that some of these may be 'binding peptides' necessary in linking NADH dehydrogenase to ubiquinone reduction, analogously to the role of small peptides in linking succinate dehydrogenase to ubiquinone. The dehydrogenase isolated by the rapid method contains equimolar amounts of non-haem iron and labile sulphur, but on further manipulation non-haem iron (but no labile sulphur) is lost, resulting in ratios of S/Fe in excess of unity, as previously reported for preparations isolated by longer procedures.     

Cinnamic Acid, an Autoinducer of Its Own Biosynthesis, Is Processed via Hca Enzymes in Photorhabdus luminescens

Photorhabdus luminescens, an entomopathogenic bacterium and nematode symbiont, has homologues of the Hca and Mhp enzymes. In Escherichia coli, these enzymes catalyze the degradation of the aromatic compounds 3-phenylpropionate (3PP) and cinnamic acid (CA) and allow the use of 3PP as sole carbon source. P. luminescens is not able to use 3PP and CA as sole carbon sources but can degrade them. Hca dioxygenase is involved in this degradation pathway. P. luminescens synthesizes CA from phenylalanine via a phenylalanine ammonia-lyase (PAL) and degrades it via the not-yet-characterized biosynthetic pathway of 3,5-dihydroxy-4-isopropylstilbene (ST) antibiotic. CA induces its own synthesis by enhancing the expression of the stlA gene that codes for PAL. P. luminescens bacteria release endogenous CA into the medium at the end of exponential growth and then consume it. Hca dioxygenase is involved in the consumption of endogenous CA but is not required for ST production. This suggests that CA is consumed via at least two separate pathways in P. luminescens: the biosynthesis of ST and a pathway involving the Hca and Mhp enzymes.     

A ferroxidase encoded by FOX1 contributes to iron assimilation under conditions of poor iron nutrition in Chlamydomonas

When the abundance of the FOX1 gene product is reduced, Chlamydomonas cells grow poorly in iron-deficient medium, but not in iron-replete medium, suggesting that FOX1-dependent iron uptake is a high-affinity pathway. Alternative pathways for iron assimilation, such as those involving ZIP family transporters IRT1 and IRT2, may be operational.     

Endogenous Siderophore 2,5-Dihydroxybenzoic Acid Deficiency Promotes Anemia and Splenic Iron Overload in Mice

Eukaryotes produce a siderophore-like molecule via a remarkably conserved biosynthetic pathway. 3-OH butyrate dehydrogenase (BDH2), a member of the short-chain dehydrogenase (SDR) family of reductases, catalyzes a rate-limiting step in the biogenesis of the mammalian siderophore 2,5-dihydroxybenzoic acid (2,5-DHBA). Depletion of the mammalian siderophore by inhibiting expression of bdh2 results in abnormal accumulation of intracellular iron and mitochondrial iron deficiency in cultured mammalian cells, as well as in yeast cells and zebrafish embryos We disrupted murine bdh2 by homologous recombination to analyze the effect of bdh2 deletion on erythropoiesis and iron metabolism. bdh2 null mice developed microcytic anemia and tissue iron overload, especially in the spleen. Exogenous supplementation with 2,5-DHBA alleviates splenic iron overload in bdh2 null mice. Additionally, bdh2 null mice exhibit reduced serum iron. Although BDH2 has been proposed to oxidize ketone bodies, we found that BDH2 deficiency did not alter ketone body metabolism in vivo. In sum, our findings demonstrate a key role for BDH2 in erythropoiesis.     

A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies

The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.     

Trapping of a reaction intermediate by tetranitromethane during catalysis by ribulose biphosphate carboxylase

Illumination at 230 K of dithionite-reduced particles results in the appearance of an EPR detectable radical 13 G wide with g = 2.0033. This radical is formed in a ratio of 2.28 (±0.5)/P700. Investigation of the time course of formation shows two components are present. One (A₁) has g = 2.0051 and the other (A_og= 2.0024. Reduction of A₁ results in an increase in reaction centre triplet formation, subsequent reduction of A_o results in a decrease of triplet formation to the base level. We propose that these components function sequentially in the transfer of electrons from P700 to the iron—sulphur acceptors.     

Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Transfer of a biosynthetic pathway between evolutionary distant organisms can create a metabolic shunt capable of bypassing the native regulation of the host organism, hereby improving the production of secondary metabolite precursor molecules for important natural products. Here, we report the engineering of Escherichia coli genes encoding the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway into the genome of Saccharomyces cerevisiae and the characterization of intermediate metabolites synthesized by the MEP pathway in yeast. Our UPLC-MS analysis of the MEP pathway metabolites from engineered yeast showed that the pathway is active until the synthesis of 2-C-methyl-d-erythritol-2,4-cyclodiphosphate, but appears to lack functionality of the last two steps of the MEP pathway, catalyzed by the [4Fe–4S] iron sulfur cluster proteins encoded by ispG and ispH. In order to functionalize the last two steps of the MEP pathway, we co-expressed the genes for the E. coli iron sulfur cluster (ISC) assembly machinery. By deleting ERG13, thereby incapacitating the mevalonate pathway, in conjunction with labeling experiments with U–¹³C₆ glucose and growth experiments, we found that the ISC assembly machinery was unable to functionalize ispG and ispH. However, we have found that leuC and leuD, encoding the heterodimeric iron–sulfur cluster protein, isopropylmalate isomerase, can complement the S. cerevisiae leu1 auxotrophy. To our knowledge, this is the first time a bacterial iron–sulfur cluster protein has been functionally expressed in the cytosol of S. cerevisiae under aerobic conditions and shows that S. cerevisiae has the capability to functionally express at least some bacterial iron–sulfur cluster proteins in its cytosol.     

Genes for iron–sulphur cluster assembly are targets of abiotic stress in rice,Oryza sativa

Iron–sulphur (Fe–S) cluster assembly occurs in chloroplasts, mitochondria and cytosol, involving dozens of genes in higher plants. In this study, we have identified 41 putative Fe–S cluster assembly genes in rice (Oryza sativa) genome, and the expression of all genes was verified. To investigate the role of Fe–S cluster assembly as a metabolic pathway, we applied abiotic stresses to rice seedlings and analysed Fe–S cluster assembly gene expression by qRT‐PCR. Our data showed that genes for Fe–S cluster assembly in chloroplasts of leaves are particularly sensitive to heavy metal treatments, and that Fe–S cluster assembly genes in roots were up‐regulated in response to iron toxicity, oxidative stress and some heavy metal assault. The effect of each stress treatment on the Fe–S cluster assembly machinery demonstrated an unexpected tissue or organelle specificity, suggesting that the physiological relevance of the Fe–S cluster assembly is more complex than thought. Furthermore, our results may reveal potential candidate genes for molecular breeding of rice.     

Changes in Liver Proteome Expression of Senegalese Sole (Solea senegalensis) in Response to Repeated Handling Stress

The Senegalese sole, a high-value flatfish, is a good candidate for aquaculture production. Nevertheless, there are still issues regarding this species’ sensitivity to stress in captivity. We aimed to characterize the hepatic proteome expression for this species in response to repeated handling and identify potential molecular markers that indicate a physiological response to chronic stress. Two groups of fish were reared in duplicate for 28?days, one of them weekly exposed to handling stress (including hypoxia) for 3?min, and the other left undisturbed. Two-dimensional electrophoresis enabled the detection of 287 spots significantly affected by repeated handling stress (Wilcoxon–Mann–Whitney U test, p?<?0.05), 33 of which could be reliably identified by peptide mass spectrometry. Chronic exposure to stress seems to have affected protein synthesis, folding and turnover (40S ribosomal protein S12, cathepsin B, disulfide-isomerase A3 precursor, cell-division cycle 48, and five distinct heat shock proteins), amino acid metabolism, urea cycle and methylation/folate pathways (methionine adenosyltransferase I α, phenylalanine hydroxylase, mitochondrial agmatinase, serine hydroxymethyltransferase, 3-hydroxyanthranilate 3,4-dioxygenase, and betaine homocysteine methyltransferase), cytoskeletal (40S ribosomal protein SA, α-actin, β-actin, α-tubulin, and cytokeratin K18), aldehyde detoxification (aldehyde dehydrogenase 4A1 family and aldehyde dehydrogenase 7A1 family), carbohydrate metabolism and energy homeostasis (fatty acid-binding protein, enolase 3, enolase 1, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, aconitase 1, mitochondrial ATP synthase α-subunit, and electron-transfer flavoprotein α polypeptide), iron and selenium homeostasis (transferrin and selenium binding protein 1), steroid hormone metabolism (3-oxo-5-β-steroid 4-dehydrogenase), and purine salvage (hypoxanthine phosphoribosyltransferase). Further characterization is required to fully assess the potential of these markers for the monitoring of fish stress response to chronic stressors of aquaculture environment.     

Specific inhibition of lignification breaks hypersensitive resistance of wheat to stem rust

When highly resistant wheat (Triticum aestivum L.) varieties are infected by an avirulent race of the stem rust fungus (Puccinia graminis Pers. f. sp. tritici Erics. and E. Henn.), penetrated host cells undergo rapid necrotization. This hypersensitive cell death is correlated with cellular lignification which efficiently restricts further fungal growth. Three competitive inhibitors of phenylalanine ammonia-lyase, the first enzyme of the general phenylpropanoid pathway and, thus, of lignin biosynthesis, namely α-aminooxyacetate, α-aminooxy-β-phenylpropionic acid, and (1-amino-2-phenylethyl)phosphonic acid, and two highly specific irreversible suicide inhibitors of the lignification-specific enzyme cinnamyl-alcohol dehydrogenase, namely N(O-aminophenyl)sulfinamoyl-tertiobutyl acetate and N(O-hydroxyphenyl)sulfinamoyl-tertiobutyl acetate, were applied to genetically resistant wheat plants prior to inoculation with stem rust. Treatment with any of these inhibitors decreased the frequency of lignified necrotic host cells and concomitantly led to increased fungal growth. The cinnamyl-alcohol dehydrogenase inhibitors were generally more effective than the phenylalanine ammonia-lyase inhibitors, occasionally allowing some sporulation to occur on the resistant wheat leaves. These results clearly point to a causal relationship between the formation of lignin precursors and the resistance of wheat to stem rust.     

Evaluation of the solubility of a range of copper sources and the effects of iron & sulphur on copper solubility under rumen simulated conditions

BackgroundAntagonisms exist in vivo which inhibit copper bioavailability in ruminants. Although the antagonism between iron, sulphur and copper has been well observed in vivo in practice the mechanism by which it acts has not yet been elucidated, nor the compound it creates identified. This results in problems when trying to optimise supplementation to prevent the interaction from occurring or provide a copper source which is able to negate its effects. This work aims to establish if the antagonism between sulphur, iron and copper could be elicited under in vitro rumen replicated conditions and using a range of copper sources to investigate any differences in their participation in the interaction.MethodsRumen simulated conditions were used to test solubility as a proxy for bioavailability of different copper sources. Sources from ionic, hydroxy and organic compounds were tested in de-ionised water and warmed, strained rumen fluid which mimicked duration, agitation, temperature and pH of the rumen.ResultsAll copper sources were less soluble in rumen fluid than in de-ionised water. The addition of sulphide, alone or as part of a sulphur mix with sulphate produced a pronounced reduction in solubility on each of the copper sources. The most soluble were the greatest affected.ConclusionThere was no indication that an in insoluble compound containing copper and iron was formed under these conditions. The intricacy of the in vivo rumen is required to elicit the reaction between copper, iron and sulphur.     

Simultaneous Involvement of a Tungsten-Containing Aldehyde:Ferredoxin Oxidoreductase and a Phenylacetaldehyde Dehydrogenase in Anaerobic Phenylalanine Metabolism

Anaerobic phenylalanine metabolism in the denitrifying betaproteobacterium Aromatoleum aromaticum is initiated by conversion of phenylalanine to phenylacetate, which is further metabolized via benzoyl-coenzyme A (CoA). The formation of phenylacetate is catalyzed by phenylalanine transaminase, phenylpyruvate decarboxylase, and a phenylacetaldehyde-oxidizing enzyme. The presence of these enzymes was detected in extracts of cells grown with phenylalanine and nitrate. We found that two distinct enzymes are involved in the oxidation of phenylacetaldehyde to phenylacetate, an aldehyde:ferredoxin oxidoreductase (AOR) and a phenylacetaldehyde dehydrogenase (PDH). Based on sequence comparison, growth studies with various tungstate concentrations, and metal analysis of the enriched enzyme, AOR was shown to be a tungsten-containing enzyme, necessitating specific cofactor biosynthetic pathways for molybdenum- and tungsten-dependent enzymes simultaneously. We predict from the genome sequence that most enzymes of molybdopterin biosynthesis are shared, while the molybdate/tungstate uptake systems are duplicated and specialized paralogs of the sulfur-inserting MoaD and the metal-inserting MoeA proteins seem to be involved in dedicating biosynthesis toward molybdenum or tungsten cofactors. We also characterized PDH biochemically and identified both NAD⁺ and NADP⁺ as electron acceptors. We identified the gene coding for the enzyme and purified a recombinant Strep-tagged PDH variant. The homotetrameric enzyme is highly specific for phenylacetaldehyde, has cooperative kinetics toward the substrate, and shows considerable substrate inhibition. Our data suggest that A. aromaticum utilizes PDH as the primary enzyme during anaerobic phenylalanine degradation, whereas AOR is not essential for the metabolic pathway. We hypothesize a function as a detoxifying enzyme if high aldehyde concentrations accumulate in the cytoplasm, which would lead to substrate inhibition of PDH.     

Oxidative inactivation of reduced NADP-generating enzymes in E. coli: iron-dependent inactivation with affinity cleavage of NADP-isocitrate dehydrogenase

Treatment of E. coli extract with iron/ascorbate preferentially inactivated NADP-isocitrate dehydrogenase without affecting glucose-6-phosphate dehydrogenase. NADP-Isocitrate dehydrogenase required divalent metals such as Mg²⁺, Mn²⁺ or Fe²⁺ ion. Iron/ascorbate-dependent inactivation of the enzyme was accompanied with the protein fragmentation as judged by SDS-PAGE. Catalase protecting the enzyme from the inactivation suggests that hydroxyl radical is responsible for the inactivation with fragmentation. TOF-MS analysis showed that molecular masses of the enzyme fragments were 36 and 12, and 33 and 14 kDa as minor components. Based on the amino acid sequence analyses of the fragments, cleavage sites of the enzyme were identified as Asp307-Tyr308 and Ala282-Asp283, which are presumed to be the metal-binding sites. Ferrous ion bound to the metal-binding sites of the E. coli NADP-isocitrate dehydrogenase may generate superoxide radical that forms hydrogen peroxide and further hydroxyl radical, causing inactivation with peptide cleavage of the enzyme. Oxidative inactivation of NADP-isocitrate dehydrogenase without affecting glucose 6-phosphate dehydrogenase shows only a little influence on the antioxidant activity supplying NADPH for glutathione regeneration, but may facilitate flux through the glyoxylate bypass as the biosynthetic pathway with the inhibition of the citric acid cycle under aerobic growth conditions of E. coli.