Reduced marine phytoplankton sulphur emissions in the Southern Ocean during the past seven glacials.

Marine biogenic sulphur affects Earth's radiation budget and may be an indicator of primary productivity in the Southern Ocean, which is closely related to atmospheric CO2 variability through the biological pump. Previous ice-core studies in Antarctica show little climate dependence of marine biogenic sulphur emissions and hence primary productivity, contradictory to marine sediment records. Here we present new 720,000-year ice core records from Dome Fuji in East Antarctica and show that a large portion of non-sea-salt sulphate, which was traditionally used as a proxy for marine biogenic sulphate, likely originates from terrestrial dust during glacials. By correcting for this, we make a revised calculation of biogenic sulphate and find that its flux is reduced in glacial periods. Our results suggest reduced dimethylsulphide emissions in the Antarctic Zone of the Southern Ocean during glacials and provide new evidence for the coupling between climate and the Southern Ocean sulphur cycle.

PRESS: PRotEin S-Sulfenylation server.

MOTIVATION: Transient S-sulfenylation of cysteine thiols mediated by reactive oxygen species plays a critical role in pathology, physiology and cell signaling. Therefore, discovery of new S-sulfenylated sites in proteins is of great importance towards understanding how protein function is regulated upon redox conditions. RESULTS: We developed PRESS (PRotEin S-Sulfenylation) web server, a server which can effectively predict the cysteine thiols of a protein that could undergo S-sulfenylation under redox conditions. We envisage that this server will boost and facilitate the discovery of new and currently unknown functions of proteins triggered upon redox conditions, signal regulation and transduction, thus uncovering the role of S-sulfenylation in human health and disease. AVAILABILITY AND IMPLEMENTATION: The PRESS web server is freely available at http://press-sulfenylation.cse.uoi.gr/ CONTACTS: agtzakos@gmail.com or gtzortzi@cs.uoi.gr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs.

UNLABELLED: S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (-SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most of its physiological activities occur under control of S-hydroxylation. Therefore, discriminating the substrate site of S-sulfenylated proteins is an essential task in computational biology for the furtherance of protein structures and functions. Research into S-sulfenylated protein is currently very limited, and no dedicated tools are available for the computational identification of SOH sites. Given a total of 1096 experimentally verified S-sulfenylated proteins from humans, this study carries out a bioinformatics investigation on SOH sites based on amino acid composition and solvent-accessible surface area. A TwoSampleLogo indicates that the positively and negatively charged amino acids flanking the SOH sites may impact the formulation of S-sulfenylation in closed three-dimensional environments. In addition, the substrate motifs of SOH sites are studied using the maximal dependence decomposition (MDD). Based on the concept of binary classification between SOH and non-SOH sites, Support vector machine (SVM) is applied to learn the predictive model from MDD-identified substrate motifs. According to the evaluation results of 5-fold cross-validation, the integrated SVM model learned from substrate motifs yields an average accuracy of 0.87, significantly improving the prediction of SOH sites. Furthermore, the integrated SVM model also effectively improves the predictive performance in an independent testing set. Finally, the integrated SVM model is applied to implement an effective web resource, named MDD-SOH, to identify SOH sites with their corresponding substrate motifs. AVAILABILITY AND IMPLEMENTATION: The MDD-SOH is now freely available to all interested users at http://csb.cse.yzu.edu.tw/MDDSOH/. All of the data set used in this work is also available for download in the website. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: francis@saturn.yzu.edu.tw.

Control of oxidative posttranslational cysteine modifications: from intricate chemistry to widespread biological and medical applications.

Cysteine residues in proteins and enzymes often fulfill rather important roles, particularly in the context of cellular signaling, protein-protein interactions, substrate and metal binding, and catalysis. At the same time, some of the most active cysteine residues are also quite sensitive toward (oxidative) modification. S-Thiolation, S-nitrosation, and disulfide bond and sulfenic acid formation are processes which occur frequently inside the cell and regulate the function and activity of many proteins and enzymes. During oxidative stress, such modifications trigger, among others, antioxidant responses and cell death. The unique combination of nonredox function on the one hand and participation in redox signaling and control on the other has placed many cysteine proteins at the center of drug design and pesticide development. Research during the past decade has identified a range of chemically rather interesting, biologically very active substances that are able to modify cysteine residues in such proteins with huge efficiency, yet also considerable selectivity. These agents are often based on natural products and range from simple disulfides to complex polysulfanes, tetrahydrothienopyridines, α,ß -unsaturated disulfides, thiuramdisulfides, and 1,2-dithiole-3-thiones. At the same time, inhibition of enzymes responsible for posttranslational cysteine modifications (and their removal) has become an important area of innovative drug research. Such investigations into the control of the cellular thiolstat by thiol-selective agents cross many disciplines and are often far from trivial.

Revisiting the dissimilatory sulfate reduction pathway.

Sulfur isotopes in the geological record integrate a combination of biological and diagenetic influences, but a key control on the ratio of sulfur isotopes in sedimentary materials is the magnitude of isotope fractionation imparted during dissimilatory sulfate reduction. This fractionation is controlled by the flux of sulfur through the network of chemical reactions involved in sulfate reduction and by the isotope effect associated with each of these chemical reactions. Despite its importance, the network of reactions constituting sulfate reduction is not fully understood, with two principle networks underpinning most isotope models. In this study, we build on biochemical data and recently solved crystal structures of enzymes to propose a revised network topology for the flow of sulfur through the sulfate reduction metabolism. This network is highly branched and under certain conditions produces results consistent with the observations that motivated previous sulfate reduction models. Our revised network suggests that there are two main paths to sulfide production: one that involves the production of thionate intermediates, and one that does not. We suggest that a key factor in determining sulfur isotope fractionation associated with sulfate reduction is the ratio of the rate at which electrons are supplied to subunits of Dsr vs. the rate of sulfite delivery to the active site of Dsr. This reaction network may help geochemists to better understand the relationship between the physiology of sulfate reduction and the isotopic record it produces.

[Feasibility of sewage sludge used as filling material in permeable reactive barrier].

Permeable reactive barriers (PRB) have been used widely as an alternative technique to treatment of acid mine drainage (AMD). Selection of the appropriate filling materials is the most important procedure to application of this treatment. Batch adsorption tests and bacteria culture batch tests were conducted to assess the possibility of sewage sludge served as filling material for PRB. Results from batch adsorption tests showed that the maximum adsorption capacities of the sewage sludge were 13.62 mg x g(-1) (Zn2+) and 15.60 mg x g(-1) (Cd2+). Bacteria culture batch tests indicated that SO4(2-) concentrations in reactors decreased from initial concentrations of 700 mg x L(-1) to below 300 mg x L(-1). Sulfate removal efficiency ranged from 60% to 70%. Fe and heavy metals, including Zn and Cd, were removed completely in two reactors. This study suggested that sewage sludge is a suitable filling material for PRB.

The role of copper in cysteine oxidation: study of intra- and inter-molecular reactions in mass spectrometry.

Cysteine-containing peptide oxidation was studied both by using an inert platinum electrode and a sacrificial electrode (copper or zinc) generating metallic ions in electrospray ionization mass spectrometry (ESI-MS). Using peptides containing one, two and three cysteines, we have compared the different chemical and electrochemical oxidation pathways of cysteine (RS(-II)H) to cystine (RS(-I)S(-I)R) and to sulfenic, sulfinic and sulfonic acid (RS(0)OH, RS(II)O(2)H and RS(IV)O(3)H, respectively). In the absence of copper ions, intra-molecular reactions were the most abundant, whereas inter-molecular reactions were found to be enhanced by the presence of copper ions. These cations favor the formation of 2 : 1 (peptide : copper) complexes compared to 1 : 1 complexes, thus enhancing the formation of inter-molecular bridges. This study highlights the importance of the position of cysteine inside a peptide during disulfide bridge formation.

Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica.

The tetrathionate (Ttr) and thiosulfate (Phs) reductases of Salmonella enterica LT2, together with the polysulfide reductase (Psr) of Wolinella succinogenes, are unusual examples of enzymes containing a molybdopterin active-site cofactor since all formally catalyse sulfur-sulfur bond cleavage. This is in contrast to the oxygen or hydrogen transfer reactions exhibited by other molybdopterin enzymes. Here the catalytic specificity of Ttr and Phs has been compared using both physiological and synthetic electron-donor systems. Ttr is shown to catalyse reduction of trithionate but not sulfur or thiosulfate. In contrast, Phs cannot reduce tetrathionate or trithionate but allows whole cells to utilize elemental sulfur as an electron acceptor. Mechanisms are proposed by which the bacterium is able to utilize an insoluble sulfur substrate by means of reactions at the cytoplasmic rather than the outer membrane.

Oxoanionic or sulfur lone pair attack? The difference in reactivity of hydrogensulfite anion and neutral dimethylsulfite towards [Bu4N]2[MoO2(S2C2)CN)2)2] in the model reductive half reaction of sulfite oxidase.

pH dependent reactivity differences of dimethylsulfite towards the title complex 1 demonstrate the crucial need of oxo-anionic coordination of sulfite to the molybdenum centre of 1 in the model reductive half reaction of sulfite oxidase.

Isolation and characterization of alkaliphilic, chemolithoautotrophic, sulphur-oxidizing bacteria.

Alkaliphilic sulphur-oxidizing bacteria were isolated from samples from alkaline environments including soda soil and soda lakes. Two isolates, currently known as strains AL 2 and AL 3, were characterized. They grew over a pH range 8.0-10.4 with an optimum at 9.5-9.8. Both strains could oxidize thiosulphate, sulphide, polysulphide, elemental sulphur and tetrathionate. Strain AL 3 more actively oxidized thiosulphate and sulphide, while isolate AL 2 had higher activity with elemental sulphur and tetrathionate. Isolate AL 2 was also able to oxidize trithionate. The pH optimum for thiosulphate and sulphide oxidation was between 9-10. Some activity remained at pH 11, but was negligible at pH 7. Metabolism of tetrathionate by isolate AL 2 involved initial anaerobic hydrolysis to form sulphur, thiosulphate and sulphate in a sequence similar to that in other colourless sulphur-oxidizing bacteria. Sulphate was produced by both strains. During batch growth on thiosulphate, elemental sulphur and sulphite transiently accumulated in cultures of isolates AL 2 and AL 3, respectively. At lower pH values, both strains accumulated sulphur during sulphide and thiosulphate oxidation. Both strains contained ribulose bisphosphate carboxylase. Thiosulphate oxidation in isolate AL 3 appeared to be sodium ion-dependent. Isolate AL 2 differed from AL 3 by its high GC mol % value (65.5 and 49.5, respectively), sulphur deposition in its periplasm, the absence of carboxysomes, lower sulphur-oxidizing capacity, growth kinetics (lower growth rate and higher growth yield) and cytochrome composition.

The reaction of chicken liver sulfite oxidase with dimethylsulfite.

We have undertaken a steady-state and rapid kinetic study of the reaction of enzyme with sulfite and dimethylsulfite. Methylation of sulfite results in a significant increase in Km and Kd for the substrate in the course of steady-state and rapid reaction kinetics, respectively, but kcat and the limiting rate constant for enzyme reduction (kred) are essentially unchanged. This indicates that while substrate oxyanion groups are effective in stabilizing the Eox.S complex, the breakdown of this complex proceeds at the same rate even in their absence. The critical element of the substrate required for reactivity is a suitable lone-pair available to undertake nucleophilic attack on a Mo = O group of the active site.

Effect of pH on sulfite oxidation by Thiobacillus thiooxidans cells with sulfurous acid or sulfur dioxide as a possible substrate.

The oxidation of sulfite by Thiobacillus thiooxidans was studied at various pH values with changing concentrations of potassium sulfite. The optimal pH for sulfite oxidation by cells was a function of sulfite concentrations, rising with increasing substrate concentrations, while that by the cell extracts was unaffected. The sulfite oxidation by cells was inhibited at high sulfite concentrations, particularly at low pH values. The results from kinetic studies show that the fully protonated form of sulfite, sulfurous acid or sulfur dioxide, is the form which penetrates the cells for the oxidation.

Sulfur isotope fractionation during SO3(2-) reduction by different clostridial species.

Sulfur isotope composition patterns for sulfide evolved from cultures supplemented with 1 mM Na2SO3, suggested that an inducible dissimilatory type SO3(2-) reduction pathway, as previously found in C. pasteurianum, probably exists in many clostridial species. Data are presented for five additional species which include pathogens and nonpathogens.

Reduction of bisulfite by the trithionate pathway by cell extracts from Desulfotomaculum nigrificans.

Bisulfite was reduced to sulfide by cell extracts of Desulfotomaculum nigrificans. When trithionate was added to reaction mixtures reducing bisulfite, sulfide formation was inhibited with accumulation of thiosulfate. The thiosulfate reductase activity of cell extracts was found to be inhibited by trithionate. Trithionate alone was reduced to thiosulfate and purified bisulfite reductase (P582) was not affected by trithionate. It is concluded that the pathway for bisulfite reduction in Dt. nigrificans includes trithionate and thiosulfate as intermediate compounds.