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At least 19 recordsLinked to original sources
PubMed2006

Structural study of two proteins SigE and ORF1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox).

Microbial redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle. These reactions are mediated by phylogenetically diverse prokaryotes containing the sulfur oxidizing gene cluster (sox). The sox gene cluster of alpha-Proteobacteria comprises of at least 15 genes, which form two transcriptional units. Recently two new orfs, which code for proteins named, SigE and ORF1, were identified in Starkeya novella. Sequence analyses reveal that SigE protein has the signature sequence of ECF-type sigma factors and a helix-turn-helix (HTH) DNA binding motif whereas ORF1 is possibly an anti ECF-sigma factor, which also has the signature sequence of the dsr family of sulfate ion binding proteins. We employed homology modeling to construct the three-dimensional structures of these proteins. The model of SigE was docked on to its promoter DNA to investigate the favourable binding modes of the protein. Interactions of SigE with its anti-sigma factor ORF1 were also reported after docking these proteins. We also identified the putative sulfate ion binding residues of ORF1 by docking sulfate ion on to it. Our study provides a rational framework for understanding of the structural as well as the molecular basis of the mechanism of the regulation of sulfur oxidation reactions by SigE and ORF1 proteins via the sox operon.

Anions↗
PubMed2005

A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon.

Microbial redox reactions of inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse prokaryotes, which also take part in the extraction of metal ions from their sulfur containing ores. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 16 genes, forming two transcriptional units, viz., soxSRT and soxVWXYZABCDEFGH. SoxY is known to be a sulfur covalently binding protein, which binds sulfur anions (such as sulfate) to form SoxY-thiocysteine-S-sulfate, the first covalently bound sulfur adduct in the novel global sulfur anion oxidation cycle. SoxZ, a sulfur compound chelating protein, binds to SoxY forming a complex to which SoxB, a sulfate thiol-esterase, binds and ultimately cleaves the sulfur adduct. We employed homology modeling to construct the three-dimensional structures of the SoxY, SoxZ, and SoxB from Paracoccus pantotrophus. With the help of docking and molecular dynamics studies we have identified the residues of SoxY, SoxZ, and SoxB involved in the interaction. The probable mechanisms of the binding of SoxY with sulfate as well as the removal of sulfate from the SoxYZ complex are also established. Our study provides a rational basis to illustrate the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these industrially important organisms.

Alphaproteobacteria↗
PubMed2001

Biological leaching of heavy metals from anaerobically digested sewage sludge using indigenous sulfur-oxidizing bacteria and sulfur waste in a closed system.

The utilization of indigenous sulfur-oxidizing bacteria and sulfur waste was investigated in order to remove heavy metals from anaerobically digested sewage sludge economically. Indigenous sulfur-oxidizing bacteria existing in anaerobically digested sewage sludge were activated by adding elemental sulfur to the sludge and then the bacteria were isolated. It was found that indigenous sulfur-oxidizing bacteria could utilize sulfur waste generated by desulfurization of digestion gas as a substrate. Then, biological leaching of heavy metals from anaerobically digested sewage sludge was carried out using indigenous sulfur-oxidizing bacteria and sulfur waste. By adding sulfur waste to sewage sludge, sulfuric acid was produced by the bacteria and the sludge pH decreased. Heavy metals in sewage sludge were effectively removed owing to the decrease of pH. The optimum amount of sulfur waste added to decrease the pH sufficiently was 5g/L when the sludge concentration was 2%. It was presented that the biological leaching of heavy metals from sewage sludge can be carried out in a closed system, where all required materials are obtained in a sewage treatment plant.

Environmental Pollution↗
PubMed2005

Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle.

Microbial redox reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse prokaryotes, some of which also take part in the extraction of metal ions from their sulfur containing ores. These sulfur oxidizers oxidize inorganic sulfur compounds like sulfide, thiosulfate etc. to produce reductants that are used for carbon dioxide fixation or in respiratory electron transfer chains. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, forming two transcriptional units, viz., soxSR and soxVWXYZABCDEFGH. SoxV is known to be a CcdA homolog involved in the transport of reductants from cytoplasm to periplasm. SoxW and SoxS are periplasmic thioredoxins, which (SoxW) interact with SoxV and thereby help in the redox reactions. We have employed homology modeling to construct the three-dimensional structures of the SoxV, SoxW and SoxS proteins from Rhodovulum sulfidophilum. With the help of docking and molecular dynamics simulations we have identified the amino acid residues of these proteins involved in the interaction. The probable biochemical mechanism of the transport of reductants through the interactions of these proteins has also been investigated. Our study provides a rational basis to interpret the molecular mechanism of the biochemistry of sulfur anion oxidation reactions by these ecologically important organisms.

Alphaproteobacteria↗
PubMed2002

Kinetic studies on elemental sulfur oxidation by Acidithiobacillus ferrooxidans: sulfur limitation and activity of free and adsorbed bacteria.

The kinetics of sulfur oxidation by Acidithiobacillus ferrooxidans in shaking flasks and a 10-L reactor was studied. The observed linearity of growth and sulfur oxidation was explained by sulfur limitation. Total cell yield was not significantly different for exponential growth as compared to growth during the sulfur-limiting phase. Kinetic studies of sulfur oxidation by growing and nongrowing bacteria indicated that both free and adsorbed bacteria oxidize sulfur. Changes in the number of free bacteria rather than cells adsorbed on sulfur were better predictors of the kinetics of sulfur oxidation, indicating that the free bacteria were performing sulfur oxidation. The active growth phase always followed adsorption of bacteria on sulfur; however, the special metabolic role of adsorbed bacteria was unclear. Their activity in sulfur solubilization was considered.

Adsorption↗
PubMed2000

A soxA gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium.

A mobilizable suicide vector, pSUP5011, was used to introduce Tn5-mob in a new facultative sulfur lithotrophic bacterium, KCT001, to generate mutants defective in sulfur oxidation (Sox(-)). The Sox(-) mutants were unable to oxidize thiosulfate while grown mixotrophically in the presence of thiosulfate and succinate. The mutants were also impaired in oxidizing other reduced sulfur compounds and elemental sulfur as evident from the study of substrate oxidation by the whole cells. Sulfite oxidase activity was significantly diminished in the cell extracts of all the mutants. A soxA gene was identified from the transposon-adjacent genomic DNA of a Sox(-) mutant strain. The sequence analysis revealed that the soxA open reading frame (ORF) is preceded by a potential ribosome binding site and promoter region with -10- and -35-like sequences. The deduced nucleotide sequence of the soxA gene was predicted to code for a protein of 286 amino acids. It had a signal peptide of 26 N-terminal amino acids. The amino acid sequence showed similarity with a putative gene product of Aquifex aeolicus, soluble cytochrome c(551) of Chlorobium limicola, and the available partial SoxA sequence of Paracoccus denitrificans. The soxA-encoded product seems to be a diheme cytochrome c for KCT001 and A. aeolicus, but the amino acid sequence of C. limicola cytochrome c(551) revealed a single heme-binding region. Another transposon insertion mutation was mapped within the soxA ORF. Four other independent transposon insertion mutations were mapped in the 4.4-kb soxA contiguous genomic DNA region. The results thus suggest that a sox locus of KCT001, essential for sulfur oxidation, was affected by all these six independent insertion mutations.

Amino Acid Sequence↗
PubMed2002

Marine acidophilic sulfur-oxidizing bacterium requiring salts for the oxidation of reduced inorganic sulfur compounds.

An acidophilic sulfur-oxidizing bacterium was isolated from seawater, and designated as strain SH. Strain SH was a Gram-negative, rod-shaped and motile bacterium, which had an optimum temperature and pH value for growth of 30 degrees C and 4.0, respectively. The mol% guanine plus cytosine of the DNA was 46.0. Chemolithotrophic growth was observed with elemental sulfur and tetrathionate at pH 4.0, and was not observed with ferrous ion. The isolate was able to utilize carbon dioxide as a carbon source, and was unable to grow heterotrophically with yeast extract or glucose. The growth of strain SH was activated in medium supplemented with NaCl. However, LiCl and KCl did not sustain the growth of strain SH. The results indicate that strain SH was an acidophilic, halophilic, and obligately chemolithotrophic sulfur-oxidizing bacterium. Phylogenetic analysis based on 16S rDNA sequences indicated that strain SH had a close relationship to Acidithiobacillus thiooxidans. The oxidizing activities of sulfur and sulfite with resting cells were stimulated not only by the addition of NaCl, but also by KCl and LiCl. The oxidation of sulfite was inhibited by ionophores, carbonyl cyanide- m-chlorophenylhydrazone (CCCP), and monensin, and respiratory inhibitors, KCN and 2-heptyl-4-hydroxy-quinoline-N-oxode (HQNO).

Acidithiobacillus thiooxidans↗
PubMed2006

Isolation and characterization of Acidicaldus organivorus, gen. nov., sp. nov.: a novel sulfur-oxidizing, ferric iron-reducing thermo-acidophilic heterotrophic Proteobacterium.

Thermo-acidophilic prokaryotes isolated from geothermal sites in Yellowstone National Park were identified as novel alpha-Proteobacteria, distantly related (approximately 93% 16S rRNA gene identity) to the mesophilic acidophile Acidisphaera rubrifaciens. One of these isolates (Y008) was shown to be more thermophilic than all previously characterized acidophilic proteobacteria, with a temperature optimum for growth between 50 and 55 degrees C and a temperature maximum of 65 degrees C. Growth was observed in media maintained at pH between 1.75 and 3.0 and was fastest at pH between 2.5 and 3.0. The G + C content of Y008 was 71.8+/-0.9 mol%. The acidophile was able to grow heterotrophically on a range of organic substrates, including various monosaccharides, alcohols and amino acids and phenol, though growth on single organic compounds required the provision of one or more growth factors. The isolate oxidized sulfur to sulfuric acid in media containing yeast extract, but was not capable of autotrophic growth with sulfur as energy source. Growth occurred under aerobic conditions and also in the absence of oxygen via anaerobic respiration using ferric iron as terminal electron acceptor. Based on these genotypic and phenotypic traits, it is proposed that Y008 represents the type species of Acidicaldus organivorus, gen. nov., sp. nov.

Alphaproteobacteria↗
PubMed2005

Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation.

The sulfur-oxidizing enzyme system (Sox) of the chemotroph Paracoccus pantotrophus is composed of several proteins, which together oxidize hydrogen sulfide, sulfur, thiosulfate or sulfite and transfers the gained electrons to the respiratory chain. The hetero-dimeric cytochrome c complex SoxXA functions as heme enzyme and links covalently the sulfur substrate to the thiol of the cysteine-138 residue of the SoxY protein of the SoxYZ complex. Here, we report the crystal structure of the c-type cytochrome complex SoxXA. The structure could be solved by molecular replacement and refined to a resolution of 1.9A identifying the axial heme-iron coordination involving an unusual Cys-251 thiolate of heme2. Distance measurements between the three heme groups provide deeper insight into the electron transport inside SoxXA and merge in a better understanding of the initial step of the aerobic sulfur oxidation process in chemotrophic bacteria.

Amino Acid Sequence↗
PubMed2004

Effects of inhibitors and NaCl on the oxidation of reduced inorganic sulfur compounds by a marine acidophilic, sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH.

The effect of NaCl and the pathways of the oxidation of reduced inorganic sulfur compounds were studied using resting cells and cell-free extracts of Acidithiobacillus thiooxidans strain SH. This isolate specifically requires NaCl for growth. The oxidation of sulfur and sulfite by resting cells was strongly inhibited by 2-heptyl-4-hydroxyquinoline-N-oxide. Carbonylcyanide m-chlorophenyl-hydrazone and monensin were also relatively strong inhibitors. Thiosulfate-oxidizing activity was not inhibited by these uncouplers. Valinomycin did not inhibit the oxidation of sulfur compounds. NaCl stimulated the sulfur- and sulfite-oxidizing activities in resting cells but not in cell-free extracts. The tetrathionate-oxidizing activity in resting cells was slightly stimulated by NaCl, whereas it did not influence the thiosulfate-oxidizing activity. Sulfide oxidation was biphasic, suggesting the formation of intermediate sulfur. The initial phase of sulfide oxidation was not affected by NaCl, whereas the subsequent oxidation of sulfur in the second phase was Na+-dependent. A model is proposed for the role of NaCl in the metabolism of reduced sulfur compounds in A. thiooxidans strain SH.

Acidithiobacillus thiooxidans↗
PubMed2005

Quantification of abiotic reaction rates in mine tailings: evaluation of treatment methods for eliminating iron- and sulfur-oxidizing bacteria.

Effective treatment techniques for eliminating iron-oxidizing (IOB) and sulfur-oxidizing bacteria (SOB) are required for the comparison of abiotic and microbial sulfide oxidation rates and mechanisms in mine tailings. This study evaluates the effect of autoclaving, repeated heating, ethanol treatment, antibiotic treatment, gamma-radiation, and washing with deionized water on tailings characteristics and concentrations of IOB and SOB. Most probable number enumeration indicates that IOB and SOB were present at very low concentrations or below detection limits following treatment with all methods except rinsing and antibiotics treatment, where higher concentrations of IOB and SOB were present. The physical, chemical, and mineralogical characterization of the tailings indicated no changes in bulk mineralogy or bulk chemical composition as a result of treatment. However, an increase in oxidized sulfur species at the tailings surface, as determined by X-ray photoelectron spectroscopy, was observed for the heating, autoclaving, and antibiotics treatments. Batch weathering experiments, used to evaluate the effect of treatment on element release rates, indicated that the final element release rates (after >30 d) were similar between treated and untreated control samples. On the basis of the results of this study, experiments over relatively long periods (>30 d) are to be recommended forthe establishment of microbial and abiotic weathering rates in mill tailings samples. For the determination of abiotic reaction rates, treatment by gamma-radiation is suggested to be the most appropriate method for sulfide-rich tailings.

Anti-Bacterial Agents↗
PubMed2005

Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum.

Seven new genes designated dsrLJOPNSR were identified immediately downstream of dsrABEFHCMK, completing the dsr gene cluster of the phototrophic sulfur bacterium Allochromatium vinosum D (DSM 180(T)). Interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. While dsrR and dsrS encode cytoplasmic proteins of unknown function, the other genes encode a predicted NADPH:acceptor oxidoreductase (DsrL), a triheme c-type cytochrome (DsrJ), a periplasmic iron-sulfur protein (DsrO), and an integral membrane protein (DsrP). DsrN resembles cobyrinic acid a,c-diamide synthases and is probably involved in the biosynthesis of siro(heme)amide, the prosthetic group of the dsrAB-encoded sulfite reductase. The presence of most predicted Dsr proteins in A. vinosum was verified by Western blot analysis. With the exception of the constitutively present DsrC, the formation of Dsr gene products was greatly enhanced by sulfide. DsrEFH were purified from the soluble fraction and constitute a soluble alpha(2)beta(2)gamma(2)-structured 75-kDa holoprotein. DsrKJO were purified from membranes pointing at the presence of a transmembrane electron-transporting complex consisting of DsrKMJOP. In accordance with the suggestion that related complexes from dissimilatory sulfate reducers transfer electrons to sulfite reductase, the A. vinosum Dsr complex is copurified with sulfite reductase, DsrEFH, and DsrC. We therefore now have an ideal and unique possibility to study the interaction of sulfite reductase with other proteins and to clarify the long-standing problem of electron transport from and to sulfite reductase, not only in phototrophic bacteria but also in sulfate-reducing prokaryotes.

Bacterial Proteins↗
PubMed2005

Prokaryotic sulfur oxidation.

Recent biochemical and genomic data differentiate the sulfur oxidation pathway of Archaea from those of Bacteria. From these data it is evident that members of the Alphaproteobacteria harbor the complete sulfur-oxidizing Sox enzyme system, whereas members of the beta and gamma subclass and the Chlorobiaceae contain sox gene clusters that lack the genes encoding sulfur dehydrogenase. This indicates a different pathway for oxidation of sulfur to sulfate. Acidophilic bacteria oxidize sulfur by a system different from the Sox enzyme system, as do chemotrophic endosymbiotic bacteria.

Acidianus↗
PubMed1998

Physiology and genetics of sulfur-oxidizing bacteria.

Reduced inorganic sulfur compounds are oxidized by members of the domains Archaea and Bacteria. These compounds are used as electron donors for anaerobic phototrophic and aerobic chemotrophic growth, and are mostly oxidized to sulfate. Different enzymes mediate the conversion of various reduced sulfur compounds. Their physiological function in sulfur oxidation is considered (i) mostly from the biochemical characterization of the enzymatic reaction, (ii) rarely from the regulation of their formation, and (iii) only in a few cases from the mutational gene inactivation and characterization of the resulting mutant phenotype. In this review the sulfur-metabolizing reactions of selected phototrophic and of chemotrophic prokaryotes are discussed. These comprise an archaeon, a cyanobacterium, green sulfur bacteria, and selected phototrophic and chemotrophic proteobacteria. The genetic systems are summarized which are presently available for these organisms, and which can be used to study the molecular basis of their dissimilatory sulfur metabolism. Two groups of thiobacteria can be distinguished: those able to grow with tetrathionate and other reduced sulfur compounds, and those unable to do so. This distinction can be made irrespective of their phototrophic or chemotrophic metabolism, neutrophilic or acidophilic nature, and may indicate a mechanism different from that of thiosulfate oxidation. However, the core enzyme for tetrathionate oxidation has not been identified so far. Several phototrophic bacteria utilize hydrogen sulfide, which is considered to be oxidized by flavocytochrome c owing to its in vitro activity. However, the function of flavocytochrome c in vivo may be different, because it is missing in other hydrogen sulfide-oxidizing bacteria, but is present in most thiosulfate-oxidizing bacteria. A possible function of flavocytochrome c is discussed based on biophysical studies, and the identification of a flavocytochrome in the operon encoding enzymes involved in thiosulfate oxidation of Paracoccus denitrificans. Adenosine-5'-phosphosulfate reductase thought to function in the 'reverse' direction in different phototrophic and chemotrophic sulfur-oxidizing bacteria was analysed in Chromatium vinosum. Inactivation of the corresponding gene does not affect the sulfite-oxidizing ability of the mutant. This result questions the concept of its 'reverse' function, generally accepted for over three decades.

Aerobiosis↗
PubMed2005

Growth inhibition by tungsten in the sulfur-oxidizing bacterium Acidithiobacillus thiooxidans.

Growth of five strains of sulfur-oxidizing bacteria Acidithiobacillus thiooxidans, including strain NB1-3, was inhibited completely by 50 microM of sodium tungstate (Na(2)WO(4)). When the cells of NB1-3 were incubated in 0.1 M beta-alanine-SO(4)(2-) buffer (pH 3.0) with 100 microM Na(2)WO(4) for 1 h, the amount of tungsten bound to the cells was 33 microg/mg protein. Approximately 10 times more tungsten was bound to the cells at pH 3.0 than at pH 7.0. The tungsten binding to NB1-3 cells was inhibited by oxyanions such as sodium molybdenum and ammonium vanadate. The activities of enzymes involved in elemental sulfur oxidation of NB1-3 cells such as sulfur oxidase, sulfur dioxygenase, and sulfite oxidase were strongly inhibited by Na(2)WO(4). These results indicate that tungsten binds to NB1-3 cells and inhibits the sulfur oxidation enzyme system of the cells, and as a result, inhibits cell growth. When portland cement bars supplemented with 0.075% metal nickel and with 0.075% metal nickel and 0.075% calcium tungstate were exposed to the atmosphere of a sewage treatment plant containing 28 ppm of H(2)S for 2 years, the weight loss of the portland cement bar with metal nickel and calcium tungstate was much lower than the cement bar containing 0.075% metal nickel.

Acidithiobacillus thiooxidans↗
PubMed1991

Pulmonary effects of sulfur oxides on the surface of copper oxide aerosol.

The authors have developed a system that generates copper oxide aerosol similar to the primary emissions from smelters. The surface of the ultrafine copper oxide aerosol is coated with a layer of sulfur oxides consisting of sulfate, S(VI), and sulfite, S(IV). Guinea pigs were exposed to this sulfur oxide layered copper oxide aerosol, and pulmonary mechanical functions were measured by using the Amdur-Mead method. The concentration of sulfur oxides on the aerosol was determined by using a flame photometric detector system. Although sulfuric acid was not found in this system, S(IV) at concentrations as low as 0.36 mumol/m3 delivered as a surface layer caused prolonged changes in pulmonary mechanical functions.

Aerosols↗
PubMed1994

Phylogenetic analysis of a highly specific association between ectosymbiotic, sulfur-oxidizing bacteria and a marine nematode.

The phylogenetic relationship of chemoautotrophic, sulfur-oxidizing, ectosymbiotic bacteria growing on a marine nematode, a Laxus sp. (formerly a Catanema sp.), to known endosymbionts and free-living bacteria was determined. Comparative 16S rRNA sequencing was used to investigate the unculturable nematode epibionts, and rRNA-targeted oligonucleotide hybridization probes were used to identify the ectosymbionts in situ. Both analyses revealed a remarkably specific and stable symbiosis. Unique hybridization of a specific probe to the ectosymbionts indicated that only one species of bacteria was present and growing on the cuticle of the nematode. Distance and parsimony methods used to infer phylogenetic trees both placed the nematode ectosymbionts at the base of a branch containing chemoautotrophic, sulfur-oxidizing endosymbionts of three bivalve families and of the tube worm Riftia pachyptila. The most closely related free-living bacteria were chemoautotrophic sulfur oxidizers belonging to the genus Thiomicrospira. Furthermore, our results suggested that a second, only distantly related group of thioautotrophic endosymbionts has as its deepest branch surface-colonizing bacteria belonging to the genus Thiothrix, some of which are capable of sulfur-oxidizing chemoautotrophic growth.

Animals↗