Distribution of iron-containing superoxide dismutase in vascular plants

Superoxide dismutases (EC 1.15.1.1) in vascular plants representing different evolutionary levels were characterized using polyacrylamide gel electrophoresis. The three forms of the enzyme were distinguished from each other based on the following criteria: a) the Cu-Zn enzyme is sensitive to cyanide wherease the Fe and Mn enzymes are not; and b) the Cu-Zn and Fe enzymes are inhibited by H₂O₂ whereas the Mn enzyme is H₂O₂-resistant. Of the 43 plant families investigated, the Fe-containing superoxide dismutase was found in three families: Gingkoaceae, Nymphaceae, and Cruciferae.     

In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.)

Superoxide dismutases (SODs), members of the metalloenzymes family are most effective intracellular enzymatic antioxidant in aerobic organisms. These enzymes provide the first line of defense in plants against the toxic effects of elevated levels of reactive oxygen species (ROS) generated during various environmental stresses. The availability of high-throughput computational tools has provided better opportunities to characterize the protein features and determine their function. In the present study an attempt was made to gain an insight into the structure and evolution of subunits of SODs (Cu-Zn, Mn and Fe SODs) of rice. The 3-Dimensional structures of SODs were modeled based on available X-ray crystal structures and further validated. The primary sequence, secondary and tertiary structure analysis revealed Mn and Fe SOD to be structurally homologous while Cu-Zn SOD is un-related to either of them. Comparative structural study also revealed former two were dominated by α-helices followed by β-strands in contrast; Cu-Zn SOD dominated by β-strands. Molecular phylogeny indicated a common evolutionary origin of Mn and Fe SOD while Cu-Zn SOD may have evolved separately.     

Isolation and characterization of the iron-containing superoxide dismutase of Methanobacterium bryantii

Methanobacterium bryantii contains a single electrophoretically discernible superoxide dismutase, which constitutes 0.4% of the extractable protein. This enzyme has been purified to electrophoretic and ultracentrifugal homogeneity. It appears to be a tetramer. The subunits were tenaciously, but noncovalently bonded and were of identical size. The molecular weight of the enzyme was found to be 91,000 ± 2000. The specific activity of this enzyme was identical to that previously noted for the corresponding enzyme from Escherichia coli. The enzyme contained 2.7 atoms of Fe, 1.7 atoms of Zn, and less than 0.2 atoms Mn per tetramer. Its amino acid composition placed this enzyme with the other Mn- and Fe-containing superoxide dismutases. The M. bryantii enzyme was also similar to previously described Fe-containing superoxide dismutases in its optical and electron paramagnetic resonance spectra and in its susceptibility to inactivation by H₂O₂. The M. bryantii enzyme was ininhibited by N₃^?, but was less sensitive towards this inhibitor than other iron-containing superoxide dismutases.     

A comparison of evolutionary rates of the two major kinds of superoxide dismutase

Summary Phylogenetic trees were constructed for 25 Cu-Zn superoxide dismutases and 31 Mn/Fe superoxide dismutases. The latter set includes seven new sequences that we determined in an effort to make the two phylogenies equally representative. We analyzed all pairwise differences in each set in an attempt to estimate rates of change. As reported by others, the Cu-Zn enzyme has experienced significant changes in its evolutionary rate. In contrast, the clock for the Mn/Fe enzyme is ticking quite regularly. The comparison of these two independently evolved superoxide dismutases that catalyze the same reaction and occur together throughout much of the biological world suggests that adaptation to environmental stress is not the basis for the erratic rate of change observed in the Cu-Zn enzyme. Offprint requests to: R.F. Doolittle     

THE ROLE AND EVOLUTION OF SUPEROXIDE DISMUTASES IN ALGAE1

Superoxide dismutases (SOD) catalyze the disproportionation of the potentially destructive superoxide anion radical (O₂^??, a byproduct of aerobic metabolism) to molecular oxygen and hydrogen peroxide: 2O₂^??+2H⁺→H₂O₂+O₂. Based on metal cofactors, four known metalloforms of SOD enzymes have been identified: they contain either Fe, Mn, Cu and Zn, or Ni. Orthologs of all metalloforms are present in oxygenic photoautotrophs. The expression of SOD is highly regulated, with specific metalloforms playing an inducible protective role for specific cellular compartments. The various metalloforms of SOD are not distributed equally within either cyanobacteria or eukaryotic algae. Typically, cyanobacteria contain either an NiSOD alone or combinations of Mn and Ni or Fe and Mn metalloforms (CuZn is rare among the cyanobacteria). The bacillariophytes and rhodophytes retain an active MnSOD, whereas the chlorophytes, haptophytes, and embryophytes have either FeSOD or multiple combinations of Fe, Mn, and CuZnSODs. The NiSOD is a relatively novel SOD and has been generally excluded from evolutionary analyses. In both cyanobacteria and chlorophyte algae, the FeSOD metalloform appears to be associated with PSI, where its primary role is most likely to deactivate reactive oxygen produced by the Mehler reaction. The CuZnSOD also appears to be associated with the plastid but is phylogenetically more restricted in its distribution. In eukaryotic algae, SODs are all nuclear encoded and, based on nucleotide sequence, protein structures, and phylogenetic distributions, appear to have unique evolutionary histories arising from the lateral gene transfer of three distinct genes to the nucleus after the endosymbiotic acquisition of mitochondria and plastids. The varied phylogenetic histories and subcellular localizations suggest significantly different selection on these SOD metalloforms after the endosymbiont organelle‐to‐host gene transfer.     

Superoxide poisons mononuclear iron enzymes by causing mismetallation

Superoxide (O₂^?) is a primary agent of intracellular oxidative stress. Genetic studies in many organisms have confirmed that excess O₂^? disrupts metabolism, but to date only a small family of [4Fe‐4S] dehydratases have been identified as direct targets. This investigation reveals that in Escherichia coli O₂^? also poisons a broader cohort of non‐redox enzymes that employ ferrous iron atoms as catalytic cofactors. These enzymes were inactivated by O₂^? both in vitro and in vivo. Although the enzymes are known targets of hydrogen peroxide, the outcome with O₂^? differs substantially. When purified enzymes were damaged by O₂^? in vitro, activity could be completely restored by iron addition, indicating that the O₂^? treatment generated an apoprotein without damaging the protein polypeptide. Superoxide stress inside cells caused the progressive mismetallation of these enzymes with zinc, which confers little activity. When O₂^? stress was terminated, cells gradually restored activity by extracting zinc from the proteins. The overloading of cells with zinc caused mismetallation even without O₂^? stress. These results support a model in which O₂^? repeatedly excises iron from these enzymes, allowing zinc to compete with iron for remetallation of their apoprotein forms. This action substantially expands the physiological imprint of O₂^? stress.     

Effect of amphotericin B on membrane-associated photosynthetic reactions in maize chloroplasts.

Superoxide dismutase of anaerobic purple sulfur bacterium, Chromatium vinosum, was purified to a homogeneous state. The enzyme contains two atoms of iron per mole and has a molecular weight of 41,000. It is composed of two identical subunits. Amino acid composition, absorption spectra, and the reaction rate constant with O₂^? are also similar to those of the Fe-superoxide dismutases from aerobes. The enzyme is sensitive to hydrogen peroxide and methylene blue-sensitized photooxidation. The functional and evolutional aspects of superoxide dismutase in anaerobes are discussed.     

Concanavalin A-induced receptor redistribution on Biomphalaria glabrata hemocytes: Characterization of capping and patching responses

Exposure of rounded, glass-adherent hemocytes from a Schistosoma mansoni-susceptible (PR albino) and S. mansoni-refractory (10-R2) stock of snails, Biomphalaria glabrata, to fluoresceinlabeled concanavalin A induces a redistribution of surface membrane Con A receptors. Receptor redistribution (patching and capping) on hemocytes from both snail stocks can be characterized as (1) rapid, with maximum cap formation occurring within 15 min of lectin treatment at 22°C, (2) sodium azide sensitive, but only at relatively high inhibitor concentrations (100–200 mm^?N₃ for capping and 200 mm^?N₃ for patching inhibition), (3) pronase sensitive (partial), but trypsin resistant, and (4) generally unaffected by exposure of snails to S. mansoni miracidia 60 or 180 min prior to extraction of hemolymph (hemocyte) samples for Con A testing. Although differences in the time course of receptor redistribution are exhibited between PR albino and 10-R2 snail hemocytes, the results of experiments involving sodium azide, proteolytic enzymes, and schistosome exposure strongly suggest that Con A-binding determinants and their associated membrane components on rounded hemocytes are very similar in both susceptible and refractory Biomphalaria stocks. It is concluded that if schistosome recognition in refractory 10-R2 snails is mediated through specific hemocyte membrane components, those components associated with Con A reactivity probably are not directly involved in the recognition process.     

Structure-Function Relationships in Iron and Manganese Superoxide Dismutases

Using the complete sequences for MnSOD from Thermus thermophilus and for FeSOD from E. coli, structural models for both oxidized enzymes have been refined, the Mn protein to an R of 0.186 for all data between 10.0 and 1.8 Å, and the Fe protein to an R of 0.22 for data between 10.0 and 2.5 A. The results of the refinements support the presence of a solvent as a fifth ligand to Mn(III) and Fe(III) and a coordination geometry that is close to trigonal bipyramidal. The putative substrate-entry channel is comprised of residues from both subunits of the dimer; several basic residues that are conserved may facilitate approach of O^?₂, while other conserved residues maintain interchain packing interactions. Analysis of the azide complex of Fe(III) dismutase suggests that during turnover O^?₂ binds to the metal at a sixth coordination site without displacing the solvent ligand. Because crystals reduced with dithionitc show no evidence for displacement of the protein ligands, the redox-linked proton acceptor (C. Bull and J.A. Fee (1985), Journol of the American Chemistry Society 107, 3295–3304) is unlikely to be one of the histidines which bind the metal ion. Structural, kinetic, titration, and spectroscopic data can be accommodated in a mechanistic scheme which accounts for the differential titration behaviour of the Fe(II1) and Fc(II) enzymes at neutral and high pH.     

Crystallographic studies of azide, thiocyanate and perchlorate complexes of methemerythrin.

Difference Fourier maps of azide, thiocyanate and perchlorate complexes of methemerythrin from Themiste dyscritum have been calculated at 4 Å, 3.5 Å and 3.5 Å resolution, respectively, with phases from a refined model. N^?₃ and SCN^? bind to the Fe complex in each subunit, indicating the mode of oxygen binding and suggesting a possible route followed by the anions in reaching the complex. ClO^?₄ binds in two different locations on the non-crystallographic 2-fold axes near cysteine 9 and cysteine 50, apparently being held to the protein by peptide amides and lysine side-chains. Binding of ClO^?₄ at these locations away from the Fe complex is observed to have some effect on the active site structure.     

SODa: An Mn/Fe superoxide dismutase prediction and design server

Background  

Superoxide dismutases (SODs) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecules. We focus here on the SOD family that uses Fe or Mn as cofactor.     

Ferric and manganic superoxide dismutases in Euglena gracilis.

Iron-containing superoxide dismutase was found in the soluble fraction from Euglena gracilis and Mn-superoxide dismutase was found in the thylakoid-bound form. Two major Fe-superoxide dismutases were isolated from the soluble fraction in the homogeneous state. Their absorption spectra, molecular weights, subunit structures, and metal contents resemble those of the Fe-enzymes from procaryotes. However,the Euglena enzymes are more sensitive to heating, to denaturants, and to H₂O₂ and less sensitive to azide than are the procaryote enzymes. The amino acid composition of the Euglena enzyme differs substantially from the compositions of the enzymes from procaryotes.     

The scavenging of superoxide radical by manganous complexes: in vitro

Dialyzable manganese has been shown to be present in millimolar concentrations within cells of Lactobacillus plantarum and related lactic acid bacteria. This unusual accumulation of Mn appears to serve the same function as Superoxide dismutase (SOD), conferring hyperbaric oxygen and Superoxide tolerance on these SOD-free organisms. The form of the Mn in the lactic acid bacteria and the mechanisms whereby it protects the cell from oxygen damage are unknown. This report examines the mechanisms by which Mn catalytically scavenges O₂^?, both in the xanthine oxidase/cytochrome c SOD assay and in a number of in vitro systems relevant to the in vivo situation. In all the reaction mixtures examined, Mn(II) is first oxidized by O₂^? to Mn(III), and H₂O₂ is formed. In pyrophosphate buffer the Mn(III) thus formed is re-reduced to Mn(II) by a second O₂^?, making the reaction a true metal-catalyzed dismutation like that catalyzed by SOD. Alternatively, if the reaction takes place in orthophosphate or a number of other buffers, the Mn(III) is preferentially reduced largely by reductants other than O₂^?, such as thiols, urate, hydroquinone, or H₂O₂. H₂O₂, a common product of the lactic acid bacteria, reacted rapidly with Mn(III) to form O₂, apparently without intermediate O₂ release. Free hexaquo Mn(II) ions were shown by electron spin resonance spectroscopy and activity assays in noncomplexing buffers to be poorly reactive with O₂^?. In contrast, Mn(II) formed complexes having a high catalytic activity in scavenging O₂^? with a number of organic acids, including malate, pyruvate, propionate, succinate, and lactate, with the Mn-lactate complex showing the greatest activity.     

Purification and characterization of Cu-Zn superoxide dismutases from mungbean (Vigna radiata) seedlings

Mungbean contains three isoenzymes of superoxide dismutase designated isoenzyme I, II and III. The two cytosolic superoxide dismutases (I and II) were purified to homogeneity by ammonium sulphate fractionation, ion exchange chromatography on diethylaminoethyl cellulose, gel filtration and preparative polyacrylamide.gel electrophoresis. The molecular weights of isoenzyme I and isoenzyme II were determined to be 33,000 and 31,600 respectively. The subunit molecular weight was approximately 16,000 indicating that the isoenzymes contained two identical subunits. The ultra-violet absorption spectra revealed a maximum at 258–264 nm for the two isoenzymes. Superoxide dismutase I and II were inhibited to different extents by metal chelators. Isoenzyme I was more sensitive to inhibition by cyanide and azide, while isoenzyme II was more susceptible to inhibition by diethyldithiocarbamate ando-phenanthroline. Both the isoenzymes exhibited similar denaturation profiles with heat, guanidinium chloride and urea. The denaturation with urea and guanidinium chloride was reversible. The two copper-zinc enzymes were more stable towards thermal inactivation compared to manganese and iron superoxide dismutases from other sources. The results indicate that the two isoenzymes differ from each other only with respect to charge and sensitivity towards metal chelators.     

Superoxide Dismutase Activity in Needles of Norwegian Spruce Trees (Picea abies L.)

The activity of superoxide dismutase was investigated in needles of spruce trees. To obtain maximum activity, needles were homogenized in the presence of Triton X-100 and polyvinylpyrrolidone. Superoxide dismutase activity was measured in dialyzed extracts with a modified epinephrine assay (HP Misra, I Fridovich [1972] J Biol Chem 247: 3170-3175) at pH 10.2. The extracts contained 70 to 120 units of superoxide dismutase per milligram protein. One unit of superoxide dismutase was completely inhibited in the presence of 20 micromolar NaCN. On native polyacrylamide gels three electromorphs were visualized after staining for activity. All three species were sensitive to CN⁻ and H₂O₂ and were therefore assumed to be Cu/Zn-superoxide dismutases. Superoxide dismutase activity was dependent on the age of the needles and declined by approximately 25% within 3 to 4 years.     

Respective role of superoxide and hydroxyl radical in the activity of the reconstituted microsomal ethanol-oxidizing system.

Superoxide dismutase, a scavenger of O^?₂. does not affect the rate of ethanol oxidation in a reconstituted system containing purified cytochrome P-450, NADPH-cytochrome c reductase, and dilauroyl l-3-phosphatidyl choline. The same concentration of Superoxide dismutase (50 μg/ml) completely abolishes the oxidation of epinephrine in this reconstituted system and ethanol oxidation by the xanthine-xanthine oxidase. Ethanol is not oxidized by the reconstituted system when NADPH is replaced by H₂O₂ but the addition of H₂O₂ to this sytem containing NADPH accelerates ethanol oxidation. This increase is abolished by the addition of Superoxide dismutase. Hydroxyl radical scavengers (50 mm dimethylsulfoxide, 100 mm benzoate, 100 mm mannitol, 20 mm thiourea) diminish the oxidation of ethanol in the reconstituted system by 48 to 76%. Thus hydroxyl radical may participate in the activity of reconstituted ethanol-oxidizing system, whereas Superoxide is not involved.     

Differential responses to cadmium induced oxidative stress in marine macroalga Ulva lactuca (Ulvales, Chlorophyta)

This study describes various biochemical processes involved in the mitigation of cadmium toxicity in green alga Ulva lactuca. The plants when exposed to 0.4 mM CdCl₂ for 4 days showed twofold increase in lipoperoxides and H₂O₂ content that collectively decreased the growth and photosynthetic pigments by almost 30% over the control. The activities of antioxidant enzymes such as superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR) and glutathione peroxidase (GPX) enhanced by twofold to threefold and that of catalase (CAT) diminished. Further, the isoforms of these enzymes, namely, Mn-SOD (~85 kDa), GR (~180 kDa) and GPX (~50 kDa) responded specifically to Cd²⁺ exposure. Moreover, the contents of reduced glutathione (3.01 fold) and ascorbate (1.85 fold) also increased substantially. Lipoxygenase (LOX) activity increased by two fold coupled with the induction of two new isoforms upon Cd²⁺ exposure. Among the polyunsaturated fatty acids, although n ? 3 PUFAs and n ? 6 PUFAs (18:3n ? 6 and C18:2n ? 6) showed relatively higher contents than control, the latter ones showed threefold increase indicating their prominence in controlling the cadmium stress. Both free and bound soluble putrescine increased noticeably without any change in spermidine. In contrast, spermine content reduced to half over control. Among the macronutrients analysed in exposed thalli, the decreased K content was accompanied by higher Na and Mn with no appreciable change in Ca, Mg, Fe and Zn. Induction of antioxidant enzymes and LOX isoforms together with storage of putrescine and n ? 6 PUFAs in cadmium exposed thallus in the present study reveal their potential role in Cd²⁺ induced oxidative stress in U. lactuca.     

Manganese application alleviates the water deficit-induced decline of N2 fixation

Water deficit is a very serious constraint on N₂ fixation rates and grain yield of soybean (Glycine max Merr.). Ureides are transported from the nodules and they accumulate in the leaves during soil drying. This accumulation appears responsible for a feedback mechanism on nitrogen fixation, and it is hypothesized to result from a decreased ureide degradation in the leaf. One enzyme involved in the ureide degradation, allantoate amidohydrolase, is manganese (Mn) dependent. As Mn deficiency can occur in soils where soybean is grown, this deficiency may aggravate soybean sensitivity to water deficit. In situ ureide breakdown was measured by incubating soybean leaves in a 5 mol m ^{? 3} allantoic acid solution for 9 h before sampling leaf discs in which remnant ureide was measured over time. In situ ureide breakdown was dramatically decreased in leaves from plants grown without Mn. At the plant level, allantoic acid application in the nutrient solution of hydroponically grown soybean resulted in a higher accumulation of ureide in leaves and lower acetylene reduction activity (ARA) by plants grown with 0 mol m ^{? 3} Mn than those grown with 6·6 mol m ^{? 3} Mn. Those plants grown with 6·6 mol m ^{? 3} Mn in comparison with those grown with 52·8 mol m ^{? 3} Mn had, in turn, higher accumulated ureide and lower ARA. To determine if Mn level also influenced N₂ fixation sensitivity to water deficit, a dry‐down experiment was carried out by slowly dehydrating plants that were grown in soil under four different Mn nutritions. Plants receiving no Mn had the lowest leaf Mn concentration, 11·9 mg kg ^{? 1}, and had N₂ fixation more sensitive to water deficit than plants treated with Mn in which leaf Mn concentration was in the range of 21–33 mg kg ^{? 1}. The highest Mn treatments increased leaf Mn concentration to 37·5 mg kg ^{? 1} and above but did not delay the decline of ARA with soil drying, although these plants showed a significant increase in ARA under well‐watered conditions.     

Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity

Superoxide dismutases (SODs) are a crucial class of enzymes in the combat against intracellular free radical damage. They eliminate superoxide radicals by converting them into hydrogen peroxide and oxygen. In spite of their very different life cycles and infection strategies, the human parasites Plasmodium falciparum, Trypanosoma cruzi and Trypanosoma brucei are known to be sensitive to oxidative stress. Thus the parasite Fe‐SODs have become attractive targets for novel drug development. Here we report the crystal structures of FeSODs from the trypanosomes T. brucei at 2.0 Å and T. cruzi at 1.9 Å resolution, and that from P. falciparum at a higher resolution (2.0 Å) to that previously reported. The homodimeric enzymes are compared to the related human MnSOD with particular attention to structural aspects which are relevant for drug design. Although the structures possess a very similar overall fold, differences between the enzymes at the entrance to the channel which leads to the active site could be identified. These lead to a slightly broader and more positively charged cavity in the parasite enzymes. Furthermore, a statistical coupling analysis (SCA) for the whole Fe/MnSOD family reveals different patterns of residue coupling for Mn and Fe SODs, as well as for the dimeric and tetrameric states. In both cases, the statistically coupled residues lie adjacent to the conserved core surrounding the metal center and may be expected to be responsible for its fine tuning, leading to metal ion specificity. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Effects of azide on the S2 state EPR signals from Photosystem II

The anion azide, N₃ ^-, has been previously found to be an inhibitor of oxygen evolution by Photosystem II (PS II) of higher plants. With respect to chloride activation, azide acts primarily as a competitive inhibitor but uncompetitive inhibition also occurs [Haddy A, Hatchell JA, Kimel RA and Thomas R (1999) Biochemistry 38: 6104–6110]. In this study, the effects of azide on PS II-enriched thylakoid membranes were characterized by electron paramagnetic resonance (EPR) spectroscopy. Azide showed two distinguishable effects on the S₂ state EPR signals. In the presence of chloride, which prevented competitive binding, azide suppressed the formation of the multiline and g = 4.1 signals concurrently, indicating that the normal S₂ state was not reached. Signal suppression showed an azide concentration dependence that correlated with the fraction of PS II centers calculated to bind azide at the uncompetitive site, based on the previously determined inhibition constant. No evidence was found for an effect of azide on the Fe(II)Q_A ^- signals at the concentrations used. This result is consistent with placement of the uncompetitive site on the donor side of PS II as suggested in the previous study. In chloride-depleted PS II-enriched membranes azide and fluoride showed similar effects on the S₂ state EPR signals, including a notable increase and narrowing of the g = 4.1 signal. Comparable effects of other anions have been described previously and apparently take place through the chloride-competitive site. The two azide binding sites described here correlate with the results of other studies of Lewis base inhibitors.This revised version was published online in October 2005 with corrections to the Cover Date.