Transcriptional and post-transcriptional regulation by nickel of sodN gene encoding nickel-containing superoxide dismutase from Streptomyces coelicolor Müller

In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation

The importance of cellular low molecular weight ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of nickel-dependent superoxide dismutase (NiSOD) from Streptomyces coelicolor. In vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota

The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.

Molecular characterization, immune responses, and functional activities of manganese superoxide dismutase in disk abalone (Haliotis discus discus)

Superoxide dismutases (SODs) are metalloenzymes that convert superoxide radicals to H₂O₂ and O₂. Although SODs have been extensively studied in mammals and other species, comparative studies in invertebrates, such as abalones, are lacking. Here, we aimed to characterize manganese superoxide dismutase in disk abalone (Haliotis discus discus) (AbMnSOD) by assessing its transcriptional levels at different embryonic developmental stages. Additionally, the temporal expression of AbMnSOD in different abalone tissues in response to bacterial, viral, and pathogen-associated molecular pattern (PAMP) stimuli was investigated. SOD activity was measured at various recombinant protein concentrations via the xanthine oxidase/WST-1 system. Cell viability upon exposure to H₂O₂, wound healing ability, and subcellular localization were determined in AbMnSOD-transfected cells. AbMnSOD was 681 bp long and contained the SOD-A domain. AbMnSOD expression was higher at the trochophore stage than at the other stages. When challenged with immune stimulants, AbMnSOD showed the highest expression at 6 h post-injection (p.i.) for all stimulants except lipopolysaccharides. In the gills, the highest AbMnSOD expression was observed at 6 h p.i., except for the Vibrio parahaemolyticus challenge. Recombinant AbMnSOD showed concentration-dependent xanthine oxidase activity. Furthermore, AbMnSOD-transfected cells survived H₂O₂-induced apoptosis and exhibited significant wound gap closure. As expected, AbMnSOD was localized in the mitochondria of the cells. Our findings suggest that AbMnSOD is an essential antioxidant enzyme that participates in regulating developmental processes and defense mechanisms against oxidative stress in hosts.

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.

Processing of Metals and Metalloids by Actinobacteria: Cell Resistance Mechanisms and Synthesis of Metal(loid)-Based Nanostructures

Metal(loid)s have a dual biological role as micronutrients and stress agents. A few geochemical and natural processes can cause their release in the environment, although most metal-contaminated sites derive from anthropogenic activities. Actinobacteria include high GC bacteria that inhabit a wide range of terrestrial and aquatic ecological niches, where they play essential roles in recycling or transforming organic and inorganic substances. The metal(loid) tolerance and/or resistance of several members of this phylum rely on mechanisms such as biosorption and extracellular sequestration by siderophores and extracellular polymeric substances (EPS), bioaccumulation, biotransformation, and metal efflux processes, which overall contribute to maintaining metal homeostasis. Considering the bioprocessing potential of metal(loid)s by Actinobacteria, the development of bioremediation strategies to reclaim metal-contaminated environments has gained scientific and economic interests. Moreover, the ability of Actinobacteria to produce nanoscale materials with intriguing physical-chemical and biological properties emphasizes the technological value of these biotic approaches. Given these premises, this review summarizes the strategies used by Actinobacteria to cope with metal(loid) toxicity and their undoubted role in bioremediation and bionanotechnology fields.

SrnR from Streptomyces griseus is a nickel-binding transcriptional activator

Nickel ions are crucial components for the catalysis of biological reactions in prokaryotic organisms. As an uncontrolled nickel trafficking is toxic for living organisms, nickel-dependent bacteria have developed tightly regulated strategies to maintain the correct intracellular metal ion quota. These mechanisms require transcriptional regulator proteins that respond to nickel concentration, activating or repressing the expression of specific proteins related to Ni(II) metabolism. In Streptomyces griseus, a Gram-positive bacterium used for antibiotic production, SgSrnR and SgSrnQ regulate the nickel-dependent antagonistic expression of two superoxide dismutase (SOD) enzymes, a Ni-SOD and a FeZn-SOD. According to a previously proposed model, SgSrnR and SgSrnQ form a protein complex in which SgSrnR works as repressor, binding directly to the promoter of the gene coding for FeZn-SOD, while SgSrnQ is the Ni(II)-dependent co-repressor. The present work focuses on the determination of the biophysical and functional properties of SgSrnR. The protein was heterologously expressed and purified from Escherichia coli. The structural and metal-binding analysis, carried out by circular dichroism, light scattering, fluorescence and isothermal titration calorimetry, showed that the protein is a well-structured homodimer, able to bind nickel with moderate affinity. DNase I footprinting and β-galactosidase gene reporter assays revealed that apo-SgSrnR is able to bind its DNA operator and activates a transcriptional response. The structural and functional properties of this protein are discussed relatively to its role as a Ni(II)-dependent sensor.

Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase

BACKGROUND

Streptomyces seoulensis has contributed to the discovery and initiation of extensive research into nickel superoxide dismutase (NiSOD), a unique type of superoxide dismutase found in actinomycetes. Still so far, there is no information about whole genome sequence of this strain.

OBJECTIVE

To investigate complete genome sequence and perform bioinformatic analyses for genomic functions related with nickel-associated genes.

METHODS

DNA was extracted using the Wizard Genomic DNA Purification Kit then sequenced using a Pacific Biosciences SMRT cell 8Pac V3 DNA Polymerase Binding Kit P6 with the PacBiov2 RSII platform. We assembled the PacBio long-reads with the HGAP3 pipeline.

RESULTS

We obtained complete genome sequence of S. seoulensis, which comprises a 6,339,363 bp linear chromosome. While analyzing the genome to annotate the genomic function, we discovered the nickel-associated genes. We observed that the sodN gene encoding for NiSOD is located adjacent to the sodX gene, which encodes for the nickel-type superoxide dismutase maturation protease. In addition, several nickel-associated genes and gene clusters-nickel-responsive regulator, nickel uptake transporter, nickel-iron [NiFe]-hydrogenase and other putative genes were also detected. Strain specific genes were discovered through a comparative analysis of S. coelicolor and S. griseus. Further bioinformatic analyses revealed that this strain encodes at least 22 putative biosynthetic gene clusters, thereby implying that S. seoulensis has the potential to produce novel bioactive compounds.

CONCLUSION

We annotated the genome and determined nickel-associated genes and gene clusters and discovered biosynthetic gene clusters for secondary metabolites implying that S. seoulensis produces novel types of bioactive compounds.

Debaryomyces hansenii up regulates superoxide dismutase gene expression and enhances the immune response and survival in Pacific red snapper (Lutjanus peru) leukocytes after Vibrio parahaemolyticus infection

Application of yeast is increasing to improve welfare and promotes growth in aquaculture. The halotolerant yeast Debaryomyces hansenii is normally a non-pathogenic yeast with probiotic properties and potential source of antioxidant enzymes as superoxide dismutase. Here, first, we characterized the sequence features of MnSOD and icCu/ZnSOD from Pacific red snapper, and second, we evaluated the potential antioxidant immune responses of the marine yeast Debaryomyces hansenii strain CBS004 in leukocytes which were then subjected to Vibrio parahaemolyticus infection. In silico analysis revealed that LpMnSOD consisted of 1186 bp, with an ORF of 678 bp encoding a 225 amino acid protein and LpicCu/ZnSOD consisted of 1090 bp in length with an ORF of 465 bp encoding a 154 amino acid protein. Multiple alignment analyzes revealed many conserved regions and active sites among its orthologs. In vitro assays using head-kidney and spleen leukocytes immunostimulated with D. hansenii and zymosan in response to V. parahaemolyticus infection reveled that D. hansenii strain CBS004 significantly increased transcriptions of MnSOD and icCu/ZnSOD genes. Flow cytometry assay showed that D. hansenii was able to inhibit apoptosis caused by V. parahaemolyticus in the Pacific red snapper leukocytes and enhanced the phagocytic capacity in head-kidney leukocytes. Immunological assays reveled an increased in superoxide dismutase and peroxidase activities, as well as, in nitric oxide production and reactive oxygen species production (respiratory burst) in fish stimulated with D. hansenii. Finally, our results. These results strongly support the idea that marine yeast Debaryomyces hansenii strain CBS004 can stimulate the antioxidant immune mechanism in head-kidney and spleen leukocytes.

Reinventing the Wheel: The NiSOD Story

The most recently discovered SOD requires nickel in its active site – NiSOD. Among the available metals, nickel seems an unlikely redox center. This chapter discusses the protein adaptations required in order to use nickel for SOD catalysis. Cysteine ligands are employed for the first time in an SOD, to suppress the potential of the Ni(ii/iii) couple. However, this adaptation alone is not sufficient to produce an SOD, since thiolate ligands are sensitive to oxidation by H2O2 and O2. Additional adaptations include the use of two unusual backbone N-donor ligands, an amidate and the N-terminal amine. Yet merely producing a stable Ni redox center is not sufficient for SOD catalysis. A source of protons is needed to produce H2O2 and the pH-independent catalysis that is characteristic of SODs. Thus, the cysteine thiolates were also employed to provide a site for protonation. In restricting active site access, NiSOD appears to have utilized the same strategy employed by MnSOD and FeSOD – a “gateway” formed by Tyr residues. Thus, NiSOD represents evolution that converged on the same criteria for catalysis as other SODs, where the adaptations to the metal site are uniquely suited to using nickel as a redox center.

Nickel Metallochaperones: Structure, Function, and Nickel-Binding Properties

Nickel-containing enzymes catalyze a series of important biochemical processes in both prokaryotes and eukaryotes. The maturation of the enzymes requires the proper assembly of the nickel-containing active sites, which involves a battery of nickel metallochaperones that exert metal delivery and storage functions. “Cross-talk” also exists between different nickel enzyme maturation processes. This chapter summarizes the updated knowledge about the nickel chaperones based on biochemical and structural biology research, and discusses the possible nickel delivery mechanisms.

Gene Expression Characteristics and Regulation Mechanisms of Superoxide Dismutase and Its Physiological Roles in Plants under Stress

Superoxide dismutases (SODs) are key enzymes functioning as the first line of antioxidant defense by virtue of the ability to convert highly reactive superoxide radicals to hydrogen peroxide and molecular oxygen. SOD plays a central role in protecting plants against the toxic effects of reactive oxygen species generated during normal cellular metabolic activity or as a result of various environmental stresses. Our review focuses on the characteristics of expression of SOD genes, the mechanisms regulating expression of SOD genes at transcriptional, posttranscriptional, and translation levels, and their functional role(s) during development and in response to biotic or abiotic stresses. We propose two important research directions: studying SOD at the genome-wide or proteome-wide level, and improving plant stress tolerances by selecting varieties using transgenic technology.

Effects of salinity change on two superoxide dismutases (SODs) in juvenile marbled eel Anguilla marmorata

Salinity is one of the most important factors that affect the fish growth and survival. Superoxide dismutases (SODs), as the primary antioxidant enzymes, play a first role in the process of preventing oxidative stress caused by excessive superoxide anion (O\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{2}^{-}$\end{document}2−) in living organisms. In the present study, we investigated the effects of salinity on the gene expressions as well as enzymatic activities of MnSOD and Cu/ZnSOD in gill, intestine, kidney, liver and muscle tissues of the marbled eel Anguilla marmorata. We found that the liver might possess stronger redox capacity compared with other tissues. Furthermore, the gene expressions and enzymatic activities of SODs in juvenile marbled eels could be effectively enhanced by low salinity but inhibited when the salinity was higher than the body tolerance. Our findings indicated that MnSOD and Cu/ZnSOD played vital roles in the adaptation of marbled eels to salinity variation, which contributed to the elucidation of physiological adaptation and regulatory mechanism of SODs in eels.

Regulation of a nickel–cobalt efflux system and nickel homeostasis in a soil actinobacterium Streptomyces coelicolor

In nickel-tolerantStreptomyces coelicolor, a highly nickel-sensitive regulator (Nur) for nickel uptake systems and an extremely insensitive regulator (NmtR) for a nickel efflux pump constitute the nickel homeostasis system.

Oxidative stress response in Pseudomonas putida

Pseudomonas putida is widely distributed in nature and is capable of degrading various organic compounds due to its high metabolic versatility. The survival capacity of P. putida stems from its frequent exposure to various endogenous and exogenous oxidative stresses. Oxidative stress is an unavoidable consequence of interactions with various reactive oxygen species (ROS)-inducing agents existing in various niches. ROS could facilitate the evolution of bacteria by mutating genomes. Aerobic bacteria maintain defense mechanisms against oxidative stress throughout their evolution. To overcome the detrimental effects of oxidative stress, P. putida has developed defensive cellular systems involving induction of stress-sensing proteins and detoxification enzymes as well as regulation of oxidative stress response networks. Genetic responses to oxidative stress in P. putida differ markedly from those observed in Escherichia coli and Salmonella spp. Two major redox-sensing transcriptional regulators, SoxR and OxyR, are present and functional in the genome of P. putida. However, the novel regulators FinR and HexR control many genes belonging to the E. coli SoxR regulon. Oxidative stress can be generated by exposure to antibiotics, and iron homeostasis in P. putida is crucial for bacterial cell survival during treatment with antibiotics. This review highlights and summarizes current knowledge of oxidative stress in P. putida, as a model soil bacterium, together with recent studies from molecular genetics perspectives.

Molecular cloning, tissue distribution and expression analysis of a manganese superoxide dismutase in blunt snout bream Megalobrama amblycephala

The full-length mitochondrial manganese superoxide dismutase cDNA of blunt snout bream Megalobrama amblycephala (denoted as MamMnSOD) was identified in liver using homology cloning and rapid amplification of cDNA ends. The full-length cDNA of MamMnSOD consisted of 986 bp, with an open reading frame encoding 224 amino acids, a 58-bp 5' untranslated region and a 256-bp 3' untranslated region. The deduced amino acid sequences of MamMnSOD showed high sequence homology to mitochondrial MnSODs from crustaceans. Several motifs, including three mitochondrial MnSOD signatures, amino acid residues responsible for coordinating the manganese, and the putative active center, were almost completely conserved in the deduced amino acid sequences of MamMnSOD. The mRNA expression of MamMnSOD in the tissues of heart, liver, spleen, kidney, muscle, intestine, and gill was examined by quantitative real-time PCR; the highest expression was in the liver. Transcription of MamMnSOD was kinetically modulated in response to nitrite stress in liver and gill tissues. The purified recombinant MamMnSOD showed potent antioxidant activity. Polyclonal antibodies generated from the recombinant product of MamMnSOD were used to specifically identify the native protein in liver of M. amblycephala. Collectively, the findings of this study strongly suggested that MamMnSOD combats oxidative stress and cellular damage induced by nitrite, by detoxifying harmful reactive oxygen species in M. amblycephala.

Distinct structural features of the peroxide response regulator from group A Streptococcus drive DNA binding

Group A streptococcus (GAS, Streptococcus pyogenes) is a strict human pathogen that causes severe, invasive diseases. GAS does not produce catalase, but has an ability to resist killing by reactive oxygen species (ROS) through novel mechanisms. The peroxide response regulator (PerR), a member of ferric uptake regulator (Fur) family, plays a key role for GAS to cope with oxidative stress by regulating the expression of multiple genes. Our previous studies have found that expression of an iron-binding protein, Dpr, is under the direct control of PerR. To elucidate the molecular interactions of PerR with its cognate promoter, we have carried out structural studies on PerR and PerR-DNA complex. By combining crystallography and small-angle X-ray scattering (SAXS), we confirmed that the determined PerR crystal structure reflects its conformation in solution. Through mutagenesis and biochemical analysis, we have identified DNA-binding residues suggesting that PerR binds to the dpr promoter at the per box through a winged-helix motif. Furthermore, we have performed SAXS analysis and resolved the molecular architecture of PerR-DNA complex, in which two 30 bp DNA fragments wrap around two PerR homodimers by interacting with the adjacent positively-charged winged-helix motifs. Overall, we provide structural insights into molecular recognition of DNA by PerR and define the hollow structural arrangement of PerR-30bpDNA complex, which displays a unique topology distinct from currently proposed DNA-binding models for Fur family regulators.

Inverse regulation of Fe- and Ni-containing SOD genes by a Fur family regulator Nur through small RNA processed from 3'UTR of the sodF mRNA

Superoxide dismutases (SODs) are widely distributed enzymes that convert superoxides to hydrogen peroxide and molecular oxygen, using various metals as cofactors. Many actinobacteria contain genes for both Ni-containing (sodN) and Fe-containing (sodF) SODs. In Streptomyces coelicolor, expression of the sodF and sodN genes is inversely regulated by nickel-specific Nur, a Fur-family regulator. With sufficient nickel, Nur directly represses sodF transcription, while inducing sodN indirectly. Bioinformatic search revealed that a conserved 19-nt stretch upstream of sodN matches perfectly with the sodF downstream sequence. We found that the sodF gene produced a stable small-sized RNA species (s-SodF) of ∼ 90 nt that harbors the anti-sodN sequence complementary to sodN mRNA from the 5'-end up to the ribosome binding site. Absence of nearby promoters and sensitivity to 5'-phosphate-specific exonuclease indicated that the s-SodF RNA is a likely processed product of sodF mRNA. The s-SodF RNA caused a significant decrease in the half-life of the sodN mRNA. Therefore, Nur activates sodN expression through inhibiting the synthesis of sodF mRNA, from which inhibitory s-SodF RNA is generated. This reveals a novel mechanism by which antagonistic regulation of one gene is achieved by small RNA processed from the 3'UTR of another gene's mRNA.

Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102

One biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, including Synechococcus sp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded by sodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome with sodN, sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter gene sodT appeared to be lethal in WH8102, so the genes for sodT and sodN in WH8102 were interrupted with the gene for Fe-SOD, sodB, and its promoter from Synechococcus sp. strain WH7803. The sodT::sodB exconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. The sodN::sodB exconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. Both sodT::sodB and sodN::sodB lines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.

Staphylococcal response to oxidative stress

Staphylococci are a versatile genus of bacteria that are capable of causing acute and chronic infections in diverse host species. The success of staphylococci as pathogens is due in part to their ability to mitigate endogenous and exogenous oxidative and nitrosative stress. Endogenous oxidative stress is a consequence of life in an aerobic environment; whereas, exogenous oxidative and nitrosative stress are often due to the bacteria's interaction with host immune systems. To overcome the deleterious effects of oxidative and nitrosative stress, staphylococci have evolved protection, detoxification, and repair mechanisms that are controlled by a network of regulators. In this review, we summarize the cellular targets of oxidative stress, the mechanisms by which staphylococci sense oxidative stress and damage, oxidative stress protection and repair mechanisms, and regulation of the oxidative stress response. When possible, special attention is given to how the oxidative stress defense mechanisms help staphylococci control oxidative stress in the host.

A manganese superoxide dismutase in blood clam Tegillarca granosa: molecular cloning, tissue distribution and expression analysis

Superoxide dismutase (SOD, EC 1.15.1.1) is one of the central enzymes involved in scavenging the high level of reactive oxygen species (ROS) by transforming O₂⁻ into hydrogen peroxide and oxygen. The full-length mitochondrial Mn-SOD cDNA of blood clam Tegillarca granosa (denoted as TgmMnSOD) was identified from haemocytes by homology cloning and rapid amplification of cDNA ends (RACE) approaches. The nucleotide sequence of TgmMnSOD consisted of 1106bp with a 5' UTR of 195bp, a 3' UTR of 227bp with a candidate polyadenylation signal sequence ATTAAA and a short polyA tail, and an open reading frame (ORF) of 648bp encoding a secreted polypeptide of 227 amino acids residues. The deduced amino acid sequence of TgmMnSOD shared significant homology to mMnSODs from other species, indicating that TgmMnSOD should be a novel member of the mMnSOD family. Several highly conserved motifs including three mMnSOD signatures, amino acid residues responsible for coordinating the manganese and the putative active center were almost completely conserved in the deduced amino acid of TgmMnSOD. The mRNA expression of TgmMnSOD in the tissues of mantle, foot, gill, haemocytes and hepatopancreas was examined by quantitative real-time PCR (qT-PCR) and mRNA transcripts of TgmMnSOD were mainly detected in hepatopancreas, haemocytes, and gill and weakly detected in the mantle and foot. The temporal expression of TgmMnSOD in haemocytes after heavy metal exposure revealed that TgmMnSOD could be induced by the three pollutants with different response profiles. The polyclonal antibodies generated from the recombinant product of TgmMnSOD could specifically identify not only the recombinant product, but also the native protein from haemocytes. The present results strongly suggested that TgmMnSOD was a cute response protein involved in marine heavy metal contaminants challenge in T. granosa.

Nickel superoxide dismutase: structural and functional roles of Cys2 and Cys6

Nickel superoxide dismutase (NiSOD) is unique among the family of superoxide dismutase enzymes in that it coordinates Cys residues (Cys2 and Cys6) to the redox-active metal center and exhibits a hexameric quaternary structure. To assess the role of the Cys residues with respect to the activity of NiSOD, mutations of Cys2 and Cys6 to Ser (C2S-NiSOD, C6S-NiSOD, and C2S/C6S-NiSOD) were carried out. The resulting mutants do not catalyze the disproportionation of superoxide, but retain the hexameric structure found for wild-type NiSOD and bind Ni(II) ions in a 1:1 stoichiometry. X-ray absorption spectroscopic studies of the Cys mutants revealed that the nickel active-site structure for each mutant resembles that of C2S/C6S-NiSOD and demonstrate that mutation of either Cys2 or Cys6 inhibits coordination of the remaining Cys residue. Mutation of one or both Cys residue(s) in NiSOD induces the conversion of the low-spin Ni(II) site in the native enzyme to a high-spin Ni(II) center in the mutants. This result indicates that coordination of both Cys residues is required to generate the native low-spin configurations and maintain catalytic activity. Analysis of the quaternary structure of the Cys mutants by differential scanning calorimetry, mass spectrometry, and size-exclusion chromatography revealed that the Cys ligands, particularly Cys2, are also important for stabilizing the hexameric quaternary structure of the native enzyme.

The structural biochemistry of the superoxide dismutases

The discovery of superoxide dismutases (SODs), which convert superoxide radicals to molecular oxygen and hydrogen peroxide, has been termed the most important discovery of modern biology never to win a Nobel Prize. Here, we review the reasons this discovery has been underappreciated, as well as discuss the robust results supporting its premier biological importance and utility for current research. We highlight our understanding of SOD function gained through structural biology analyses, which reveal important hydrogen-bonding schemes and metal-binding motifs. These structural features create remarkable enzymes that promote catalysis at faster than diffusion-limited rates by using electrostatic guidance. These architectures additionally alter the redox potential of the active site metal center to a range suitable for the superoxide disproportionation reaction and protect against inhibition of catalysis by molecules such as phosphate. SOD structures may also control their enzymatic activity through product inhibition; manipulation of these product inhibition levels has the potential to generate therapeutic forms of SOD. Markedly, structural destabilization of the SOD architecture can lead to disease, as mutations in Cu,ZnSOD may result in familial amyotrophic lateral sclerosis, a relatively common, rapidly progressing and fatal neurodegenerative disorder. We describe our current understanding of how these Cu,ZnSOD mutations may lead to aggregation/fibril formation, as a detailed understanding of these mechanisms provides new avenues for the development of therapeutics against this so far untreatable neurodegenerative pathology.

Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition

Nur, a member of the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in Streptomyces coelicolor. Here we report the 2.4-Å resolution crystal structure of Nur. It contains a unique nickel-specific metal site in addition to a nonspecific common metal site. The identification of the 6-5-6 motif of the Nur recognition box and a Nur/DNA complex model reveals that Nur mainly interacts with terminal bases of the palindrome on complex formation. This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif. The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns. Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.

Single and combined effects of nickel (Ni(II)) and cobalt (Co(II)) ions on activated sludge and on other aerobic microorganisms: a review

Nickel (N(II)) and cobalt (Co(II)) are often encountered in wastewaters. As conventional wastewater treatment may only partially remove nickel and cobalt, a large fraction of the above metals is released to the aquatic environment. Both metals have been identified as micronutrients, at trace concentrations; however, they are both microbial growth inhibitors, at relatively high concentrations. On the other hand, the combined effects (e.g.: growth stimulation or toxicity) of the above metals have been found to differ from the summation of the effects which occur when the metals are applied individually. Moreover, a number of environmental factors (e.g.: pH, biomedium composition, biomass concentration, presence of other heavy metals) can affect the microbial toxicity of the above metallic species. The present review discusses, in a systematic way, the individual and joint effects of the above heavy metals to the growth of microorganisms grown under aerobic conditions, with focus on the growth of activated sludge. Data on multi-metal toxicity are particularly useful in establishing criteria for heavy metal tolerance levels in the environment.

Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases

We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.

Redox control in actinobacteria

As most actinobacteria are obligate aerobes, they have to cope with endogenously generated reactive oxygen species, and actinobacterial pathogens have to resist oxidative attack by phagocytes. Actinobacteria also have to survive long periods under low oxygen tension; for example, Mycobacterium tuberculosis can persist in the host for years under apparently hypoxic conditions in a latent, non-replicative state. Here we focus on the regulatory switches that control actinobacterial responses to peroxide stress, disulfide stress and low oxygen tension. Other unique aspects of their redox biology will be highlighted, including the use of the pseudodisaccharide mycothiol as their major low-molecular-weight thiol buffer, and the [4Fe-4S]-containing WhiB-like proteins, which play diverse, important roles in actinobacterial biology, but whose biochemical role is still controversial.

Sample preparation for two-dimensional blue native/SDS polyacrylamide gel electrophoresis in the identification of Streptomyces coelicolor cytoplasmic protein complexes

Ammonium sulfate precipitation was tested as a sample preparation step for BN-PAGE analyses of S. coelicolor cytoplasmic protein complexes. A procedure of sample preparation compatible with two-dimensional BN/SDS-PAGE was established and used to visualize protein complexes. To validate the sample preparation procedure, representative protein complexes were identified. Several previously characterized protein complexes were rediscovered and their reported oligomeric states reconfirmed. In addition, we identified new but plausible interactions that have never been reported before. Our work provides useful reference for the wide application of BN-PAGE in protein interaction study.

Superoxide dismutases of heavy metal resistant streptomycetes

Heavy metal tolerant and resistant strains of streptomycetes isolated from a former uranium mining site were screened for their superoxide dismutase expression. From the strains tolerating high concentrations of different heavy metals, one was selected for its tolerance of concentrations of heavy metals (Ni, Cu, Cd, Cr, Mn, Zn, Fe). This strain, Streptomyces acidiscabies E13, was chosen for the purpose of superoxide dismutase analysis. Gel electrophoresis and activity staining revealed only one each of a nickel (NiSOD) and an iron (FeZnSOD) containing superoxide dismutase as shown by differential enzymatic repression studies. The gene for nickel containing superoxide dismutase, sodN, was cloned and sequenced from this strain. The genomic sequence shows 92.7% nucleotide identity and 96.1% amino acid identity to sodN of S. coelicolor. Expression can be activated by nickel as well as other heavy metals and active enzyme is produced in media lacking nickel but containing copper, iron or zinc. Thus, the selected strain is well suited for further characterization of the enzyme encoded by sodN.

Molecular cloning and characterization of Mn-superoxide dismutase from disk abalone (Haliotis discus discus)

The mitochondrial enzyme manganese superoxide dismutase (mitMn-SOD) is one of the antioxidant enzymes involved in cellular defense against oxidative stress and catalyzes the conversion of O(2)(-) into the stabler H(2)O(2). In this study, a putative gene encoding Mn-SOD from disk abalone (Haliotis discus discus, aMn-SOD) was cloned, sequenced, expressed in Escherichia coli K12(TB1) and the protein was purified using pMAL protein purification system. Sequencing resulted ORF of 681 bp, which corresponded to 226 amino acids. The protein was expressed in soluble form with molecular weight of 68 kDa including maltose binding protein and pI value of 6.5. The fusion protein had 2781 U/mg activity. The optimum temperature of the enzyme was 37 degrees C and it was active in a range of acidic pH (from 3.5 to 6.5). The enzyme activity was reduced to 50% at 50 degrees C and completely heat inactivated at 80 degrees C. The alignment of aMn-SOD amino acid sequence with Mn-SODs available in NCBI revealed that the enzyme is conserved among animals with higher than 30% identity. In comparison with human mitMn-SOD, all manganese-binding sites are also conserved in aMn-SOD (H28, H100, D185 and H189). aMn-SOD amino acid sequence was closer to that of Biomphalaria glabrata in phylogenetic analysis.

Superoxide dismutase B gene (sodB)-deficient mutants of Francisella tularensis demonstrate hypersensitivity to oxidative stress and attenuated virulence

A Francisella tularensis live vaccine strain mutant (sodB(Ft)) with reduced Fe-superoxide dismutase gene expression was generated and found to exhibit decreased sodB activity and increased sensitivity to redox cycling compounds compared to wild-type bacteria. The sodB(Ft) mutant also was significantly attenuated for virulence in mice. Thus, this study has identified sodB as an important F. tularensis virulence factor.

Nur, a nickel-responsive regulator of the Fur family, regulates superoxide dismutases and nickel transport in Streptomyces coelicolor

Nickel serves as a cofactor for various microbial enzymes including superoxide dismutase (SOD) found in Streptomyces spp. In Streptomyces coelicolor, nickel represses and induces production of Fe-containing and Ni-containing SODs, respectively, primarily at the transcriptional level. We identified the nickel-responsive regulator (Nur), a Fur (ferric-uptake regulator) homologue, which binds to the promoter region of the sodF gene encoding FeSOD in the presence of nickel. Disruption of the nur gene caused constitutive expression of FeSOD and no induction of NiSOD in the presence of nickel. The intracellular level of nickel was higher in a Deltanur mutant than in the wild type, suggesting that Nur also regulates nickel uptake in S. coelicolor. A putative nickel-transporter gene cluster (nikABCDE) was identified in the genome database. Its transcription was negatively regulated by Nur in the presence of nickel. Purified Nur protein bound to the nikA promoter region in a nickel-dependent way. These results support the action of Nur as a regulator of nickel homeostasis and antioxidative response in S. coelicolor, and add a novel nickel-responsive member to the list of versatile metal-specific regulators of the Fur family.

Nickel represses the synthesis of the nickel permease NixA of Helicobacter pylori

Nickel acquisition is necessary for urease activity, a major virulence factor of the human gastric pathogen Helicobacter pylori. NixA was identified as a specific nickel uptake system in this organism. Addition of small amounts of nickel to media strongly stimulates urea hydrolysis. On the other hand, high nickel concentrations are deleterious to cell growth. As a possible protective reaction, nickel uptake seems to be reduced in H. pylori grown in nickel-rich media. These observations led to investigations of regulation of the expression of the nickel permease NixA. We found that increasing the nickel concentration in media reduced the amount of NixA. In order to address the question of whether this phenomenon was subject to transcriptional or translational regulation, we quantified nixA mRNA from H. pylori by real-time PCR. The amount of nixA mRNA was gradually reduced five- to sevenfold in a time- and concentration-dependent manner. Repression could be measured as soon as 5 min after nickel addition, and the maximum repression occurred after 20 to 30 min. The maximum repression was obtained with an external nickel concentration of 100 microM. The observed nickel repression of NixA was dependent on nikR encoding the nickel-responsive regulatory protein NikR. In conclusion, we demonstrated that synthesis of the NixA nickel permease of H. pylori shows nickel-responsive regulation mediated by NikR to maintain the balance between effective nickel acquisition and a toxic overload.

In vivo production of active nickel superoxide dismutase from Prochlorococcus marinus MIT9313 is dependent on its cognate peptidase

Metal-dependent superoxide dismutases (SODs) with a specific requirement for a manganese or iron ion for catalytic activity and copper- and zinc-dependent enzymes are essential for detoxification of superoxide anion radicals. Genome sequence analyses predict the existence of a nickel-dependent enzyme (NiSOD) as the unique SOD in oxygen-evolving marine cyanobacteria. NiSOD activity was observed in Escherichia coli when sodN and sodX (encoding a putative peptidase) from Prochlorococcus marinus MIT9313 were coexpressed.

Copper response element and Crr1-dependent Ni(2+)-responsive promoter for induced, reversible gene expression in Chlamydomonas reinhardtii

The Cpx1 and Cyc6 genes of Chlamydomonas reinhardtii are activated in copper-deficient cells via a signal transduction pathway that requires copper response elements (CuREs) and a copper response regulator defined by the CRR1 locus. The two genes can also be activated by provision of nickel or cobalt ions in the medium. The response to nickel ions requires at least one CuRE and also CRR1 function, suggesting that nickel interferes with a component in the nutritional copper signal transduction pathway. Nickel does not act by preventing copper uptake/utilization because (i) holoplastocyanin formation is unaffected in Ni(2+)-treated cells and (ii) provision of excess copper cannot reverse the Ni-dependent activation of the target genes. The CuRE is sufficient for conferring Ni-responsive expression to a reporter gene, which suggests that the system has practical application as a vehicle for inducible gene expression. The inducer can be removed either by replacing the medium or by chelating the inducer with excess EDTA, either of which treatments reverses the activation of the target genes.

Crystal structure of nickel-containing superoxide dismutase reveals another type of active site

Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.

Role and regulation of the superoxide dismutases of Staphylococcus aureus

Staphylococcus aureus has two superoxide dismutases (SODs), encoded by the sodA and sodM genes, which inactivate harmful superoxide radicals () encountered during host infection or generated from aerobic metabolism. The transcriptional start sites have been mapped and expression analysis on reporter fusions in both genes has been carried out. Under standard growth conditions, manganese (Mn), a mineral superoxide scavenger, elevated total SOD activity but had no effect on the transcription of either gene. Transcription of sodA and sodM was most strongly induced by either internally or externally generated, respectively. Sensitivity to internally generated was linked with SodA deficiency. Mn supplementation completely rescued a sodA mutant when challenged by internally generated, and this was growth-phase-dependent. Sensitivity to externally generated stress was only observed in a sodA sodM mutant and was Mn-independent. In a mouse abscess model of infection, isogenic sodA, sodM and sodA sodM mutants had reduced virulence compared to the parental strain, showing the importance of the enzymic scavenging system for the survival of the pathogen.