Multifrequency cw-EPR investigation of the catalytic molybdenum cofactor of polysulfide reductase from<Emphasis Type="Italic"> Wolinella succinogenes</Emphasis>

Electron paramagnetic resonance (EPR) spectra of the molybdenum centre in polysulfide reductase (Psr) from Wolinella succinogenes with unusually high G-tensor values have been observed for the first time. Three different Mo(V) states have been generated (by the addition of the substrate polysulfide and different redox agents) and analysed by their G- and hyperfine tensors using multifrequency (S-, X- and Q-band) cw-EPR spectroscopy. The unusually high G-tensor values are attributed to a large number of sulfur ligands. Four sulfur ligands are assumed to arise from two pterin cofactors; one additional sulfur ligand was identified from mutagenesis studies to be a cysteine residue of the protein backbone. One further sulfur ligand is proposed for two of the Mo(V) states, based on the experimentally observed shift of the g(av) value. This sixth sulfur ligand is postulated to belong to the polysulfide substrate consumed within the catalytic reaction cycle of the enzyme. The influence of the co-protein sulfur transferase on the Mo(V) G-tensor supports this assignment.     

Carbonylation of mitochondrial aconitase with 4-hydroxy-2-(E)-nonenal: Localization and relative reactivity of addition sites

Mass spectrometry was used to investigate the effects of exposing mitochondrial aconitase (ACO2) to the membrane lipid peroxidation product, 4-hydroxy-2-(E)-nonenal (HNE). ACO2 was selected for this study because (1) it is known to be inactivated by HNE, (2) elevated concentrations of HNE-adducted ACO2 have been associated with disease states, (3) extensive structural information is available, and (4) the iron–sulfur cluster in ACO2 offers a critical target for HNE adduction. The aim of this study was to relate the inactivation of ACO2 by HNE to structural features. Initially, Western blotting and an enzyme activity assay were used to assess aggregate effects and then gel electrophoresis, in-gel digestion, and tandem mass spectrometry (MS/MS) were used to identify HNE addition sites. HNE addition reaction rates were determined for the most significant sites using the iTRAQ approach. The most reactive sites were Cys³⁵⁸, Cys⁴²¹, and Cys⁴²⁴, the three iron–sulfur cluster-coordinating cysteines, Cys⁹⁹, the closest non-ligated cysteine to the cluster, and Cys⁵⁶⁵, which is located in the cleft leading to the active site. Interestingly, both enzyme activity assay and iTRAQ relative abundance plots appeared to be trending toward horizontal asymptotes, rather than completion.     

Sulfur Metabolism in Plants: Are Trees Different?

Sulfur metabolite levels and sulfur metabolism have been studied in a significant number of herbaceous and woody plant species. However, only a limited number of datasets are comparable and can be used to identify similarities and differences between these two groups of plants. From these data, it appears that large differences in sulfur metabolite levels, as well as the genetic organization of sulfate assimilation and metabolism do not exist between herbaceous plants and trees. The general response of sulfur metabolism to internal and/or external stimuli, such as oxidative stress, seems to be conserved between the two groups of plants. Thus, it can be expected that, generally, the molecular mechanisms of regulation of sulfur metabolism will also be similar. However, significant differences have been found in fine tuning of the regulation of sulfur metabolism and in developmental regulation of sulfur metabolite levels. It seems that the homeostasis of sulfur metabolism in trees is more robust than in herbaceous plants and a greater change in conditions is necessary to initiate a response in trees. This view is consistent with the requirement for highly flexible defence strategies in woody plant species as a consequence of longevity. In addition, seasonal growth of perennial plants exerts changes in sulfur metabolite levels and regulation that currently are not understood. In this review, similarities and differences in sulfur metabolite levels, sulfur assimilation and its regulation are characterized and future areas of research are identified.     

The production and utilization of intermediary elemental sulfur during the oxidation of reduced sulfur compounds by Thiobacillus ferrooxidans

The intermediary production of elemental sulfur during the microbial oxidation of reduced sulfur compounds has frequently been reported. Thiobacillus ferrooxidans, an acidophilic chemolithoautotroph, was found to produce an insoluble sulfur compound, primarily elemental sulfur, during the oxidation of thiosulfate, trithionate, tetrathionate and sulfide. This was confirmed by light and electron microscopy. Sulfur was produced from sulfide by an oxidative step, while the production from tetrathionate was initiated by a hydrolytic step, probably followed by a series of chemical reactions. The oxidation of intermediary sulfur was severely inhibited by sulfhydryl-binding reagents such as N-ethylmaleimide, by the addition of uncouplers or after freezing and thawing of the cells, which probably damaged the cell membrane. The mechanisms behind these inhibitions have not yet been clarified. Finally, it was observed that elemental sulfur oxidation by whole cells depended on the medium composition. The absence of sulfate or selenate reduced the sulfur oxidation rate.Non-standard abbreviations NEM N-ethylmaleimide - CCCP carbonyl cyanide m-chlorophenyl hydrazone     

Chiral ligand optimization in the asymmetric zirconium-zinc transmetalation aldehyde addition reaction

The in situ hydrozirconation-transmetalation-aldehyde addition process is a convenient method for the generation of allylic alcohols. Ongoing research has focused on enhancing the enantioselectivity and substrate scope of this process. A chiral beta-amino thiol scaffold was evaluated in the addition reaction. Amino thiols tend to provide the highest ee's, in part due to the higher affinity of sulfur for zinc over zirconium. A class of valine-based thiol ligands was identified to be effective for the formation of enantiomerically enriched allylic alcohols in terms of low ligand loading and high % ee.     

Interactive effects of soil warming and nitrogen addition on fine root production of Chinese fir seedlings

Aims There have been a large number of studies on the independent separate responses of fine roots to warming and nitrogen deposition, but with contradictory reporting. Fine root production plays a critical role in ecosystem carbon, nutrient and water cycling, yet how it responds to the interactive warming and nitrogen addition is not well understood. In the present study, we aimed to examine the interactive effects of soil warming and nitrogen addition on fine root growth of 1-year-old Chinese fir (Cunninghamia lanceolata) seedlings in subtropical China.
Methods A mesocosm experiment, with a factorial design of soil warming (ambient, +5 °C) and nitrogen addition (ambient, ambient + 40 kg·hm^-2·a^-1, ambient + 80 kg·hm^-2·a^-1), was carried out in the Chenda State-owned Forest Farm in Sanming City, Fujian Province, China. Fine root production (indexed by the number of fine roots emerged per tube of one year) was measured biweekly using minirhizotrons from March of 2014 to February of 2015.
Important findings (1) The two-way ANOVA showed that soil warming had a significant effect on fine root production, while nitrogen addition and soil warming × nitrogen addition had no effect. (2) The three-way ANOVA (soil warming, nitrogen addition and diameter class) showed that soil warming, diameter class and soil warming × diameter class had significant effects on fine root production, especially for the number of fine roots in 0-1 mm diameter class that had been significantly increased by soil warming. Compared with the 1-2 mm roots, the 0-1 mm roots seemed more flexible. (3) Repeated measures of ANOVA (soil warming, nitrogen addition and season) showed that soil warming, season, soil warming × season, and soil warming × nitrogen addition × season had significant effects on fine root production. In spring, the number of fine roots was significantly increased both by soil warming and soil warming × season, while soil warming, nitrogen addition, soil warming × nitrogen addition significantly decreased fine root production in the summer. (4) Soil warming, soil layer, soil warming × soil layer had significant effects on fine root production. The number of in-growth fine roots was significantly increased by soil warming at the 20-30 cm depth only. It seemed that warming forced fine roots to grow deeper in the soil. In conclusion, soil warming significantly increased fine root production, but they had different responses and were dependent of different diameter classes, seasons and soil layers. Nitrogen addition had no effect on fine root production. Only in spring and summer, soil warming and nitrogen addition had significant interactive effects.     

Multitrophic effects of nutrient addition in upland grassland

Although the effects of nutrient enhancement on aquatic systems are well documented, the consequences of nutritional supplements on soil food webs are poorly understood, and results of past research examining bottom-up effects are often conflicting. In addition, many studies have failed to separate the effects of nutrient enrichment and the physical effects of adding organic matter. In this field study, we hypothesised that the addition of nitrogen to soil would result in a trophic cascade, through detritivores (Collembola) to predators (spiders), increasing invertebrate numbers and diversity.Nitrogen and lime were added to plots in an upland grassland in a randomised block design. Populations of Collembola and spiders were sampled by means of pitfall traps and identified to species.Seventeen species of Collembola were identified from the nitrogen plus lime (N+L) and control plots. Species assemblage, diversity, richness, evenness and total number were not affected by nutrient additions. However, there was an increase in the number of Isotomidae juveniles and Parisotoma anglicana trapped in the N+L plots.Of the 44 spider species identified, over 80% were Linyphiidae. An effect on species assemblage from the addition of N+L to the plots was observed on two of the four sampling dates (July 2002 and June 2003). The linyphiid, Oedothorax retusus, was the only species significantly affected by the treatments and was more likely to be trapped in the control plots.The increased number of juvenile Collembola, and change in community composition of spiders, were consequences of the bottom-up effect caused by nutrient inputs. However, despite efforts to eliminate the indirect effects of nutrient inputs, a reduction in soil moisture in the N+L plots cannot be eliminated as a cause of the invertebrate population changes observed. Even so, this experiment was not confounded by the physical effects of habitat structure reported in most previous studies. It provides evidence of moderate bottom-up influences of epigeic soil invertebrate food webs and distinguishes between nutrient addition and plant physical structure effects. It also emphasises the importance of understanding the effects of soil management practices on soil biodiversity, which is under increasing pressure from land development and food production.     

Oxidation of biological thiols by highly reactive disulfide-S-oxides

Oxidative stress involves the generation of a number of reactive species, among them 'reactive oxygen species' and 'reactive nitrogen species'. Recent reports have indicated that disulfide-S-monoxides (thiosulfinates) and disulfide-S-dioxides (thiosulfonates) are formed under conditions of oxidative stress. We have now been able to demonstrate that these species are highly reactive and rapidly oxidise thiols. Glutathione and cysteine were oxidised to mixed disulfides by the action of disulfide-S-oxides. Oxidative attack on the zinc/sulfur protein metallothionein with concomitant zinc release was readily accomplished by these 'reactive sulfur species' whereas hydrogen peroxide showed minimal zinc release.     

Kinetic model of elemental sulfur oxidation by Thiobacillus thiooxidans in batch slurry reactors

The kinetics of sulfur oxidation by T. thiooxidans has been studied in a batch well-mixed reactor and in shaker flasks. A mathematical model is proposed, which considers the attachment of the cells onto the sulfur particles' surface following Freundlich isotherm, growth of the attached bacteria, and growth inhibition by sulfates accumulation. Best-fit values of the model parameters have been calculated from the experimental data. Results show that the addition of dimethyl-dichloro-silane in the aerated reactor to prevent the formation of foam reduces the maximum specific growth rate of attached bacteria, probably because of the resulting changes in surface properties of the sulfur particles. The other model parameters are not significantly affected. The formation of clusters of sulfur particles has been observed at an initial sulfur concentration of 5% . This phenomenon reduces the rate of sulfur conversion due to the reduction of the total surface area of the particles, and the model therefore over-estimates the formation of sulfates. At lower initial sulfur concentration, the phenomenon has not been observed and the model simulations are then satisfactory.     

Identification of a molybdopterin-containing molybdenum cofactor in xanthine dehydrogenase from Pseudomonas aeruginosa.

Xanthine dehydrogenase has been purified from Pseudomonas aeruginosa cultured on a rich medium and induced with hypoxanthine. The enzyme was shown to contain FAD, iron sulfur centers and a molybdenum cofactor as prosthetic groups. Analysis of the molybdenum cofactor in this enzyme has revealed that the cofactor contains molybdopterin (MPT) rather than molybdopterin guanine dinucleotide or molybdopterin cytosine dinucleotide which have previously been identified in a number of molybdoenzymes of bacterial origin. The pterin cofactor in P.aeruginosa xanthine dehydrogenase was alkylated and the resulting product was identified as dicarboxamidomethyl molybdopterin. In addition, the pterin released from the enzyme by denaturation with guanidine-HCl was found to chromatograph on Sephadex G-15 with an apparent molecular weight of 350. These results document the first example of a bacterial enzyme with a molybdenum cofactor comprising molybdopterin and the metal only.     

Role of Iron and Sulfur in Pigment and Slime Formation by Pseudomonas aeruginosa

Media and an analytical scheme have been developed which allow both a qualitative and quantitative estimation of the formation of pyocyanine, related phenazines, pyorubrin, and a blue and a yellow-green fluorescent pigment by Pseudomonas aeruginosa. Use of the defined pyocyanine medium of Frank and DeMoss with sulfate or various organic sulfur sources allowed formation of pyocyanine, related phenazines, and pyorubrin. When sulfite was the sulfur source with or without iron, P. aeruginosa formed either a yellow-green or a blue fluorescent pigment. Formation of fluorescent pigments of P. aeruginosa is related to the ability of sulfite to act as a specific sulfur source. In an investigation of the role of both added iron and sulfur sources, complex patterns of pigment formation were observed. In addition to the fluorescent pigments, sulfite also supported the formation of slime by P. aeruginosa.     

The effects of heat and stannous chloride addition on the active distillation of acid volatile sulfide from pyrite-rich marine sediment samples

Iron monosulfides are important intermediates in pyrite formation, and are operationally defined as sulfides soluble in concentrated hydrochloric acid. A number of variations are currently employed in their isolation and quantification. In this study, the active distillation of acid volatile sulfide from sediment samples was studied to determine the effects of stannous chloride and heat. The addition of SnCl₂ caused recovery of sulfide to increase by 20% during distillations performed at room temperature. If distillations with SnCl₂ were then heated and boiled, recovery increased by up to 100%. Tests with 98% pure pyrite and elemental sulfur showed that these compounds were reduced to sulfide in solutions of 15% and 20% SnCI₂ in boiling 6N HCI, and that these reactions were grain size dependent. The compounds were not significantly reduced by solutions of SnCI₂ at room temperature, or by boiling 6N HCl not containing SnCl₂.     

Uridylate addition and RNA ligation contribute to the specificity of kinetoplastid insertion RNA editing

RNA editing in Trypanosoma brucei inserts and deletes uridylates (U's) in mitochondrial pre-mRNAs under the direction of guide RNAs (gRNAs). We report here the development of a novel in vitro precleaved editing assay and its use to study the gRNA specificity of the U addition and RNA ligation steps in insertion RNA editing. The 5' fragment of substrate RNA accumulated with the number of added U's specified by gRNA, and U addition products with more than the specified number of U's were rare. U addition up to the number specified occurred in the absence of ligation, but accumulation of U addition products was slowed. The 5' fragments with the correct number of added U's were preferentially ligated, apparently by adenylylated RNA ligase since exogenously added ATP was not required and since ligation was eliminated by treatment with pyrophosphate. gRNA-specified U addition was apparent in the absence of ligation when the pre-mRNA immediately upstream of the editing site was single stranded and more so when it was base paired with gRNA. These results suggest that both the U addition and RNA ligation steps contributed to the precision of RNA editing.     

Redox and addition chemistry of quinoid compounds and its biological implications

The overall biological activity of quinones is a function of the physico-chemical properties of these compounds, which manifest themselves in a critical bimolecular reaction with bioconstituents. Attempts have been made to characterize this bimolecular reaction as a function of the redox properties of quinones in relation to hydrophobic or hydrophilic environments. The inborn physico-chemical properties of quinones are discussed on the basis of their reduction potential and dissociation constants, as well as the effect of environmental factors on these properties. Emphasis is given on the effect of methyl-, methoxy-, hydroxy-, and glutathionyl substituents on the reduction potential of quinones and the subsequent electron transfer processes. The redox chemistry of quinoid compounds is surveyed in terms of a) reactions involving only electron transfer, as those accomplished during the enzymic reduction of quinones and the non-enzymic interaction with redox couples generating semiquinones, and b) nucleophilic addition reactions. The addition of nucleophiles, entailing either oxidation or reduction of the quinone, are exemplified in reactions with oxygen- or sulfur nucleophiles, respectively. The former yields quinone epoxides, whereas the latter yields thioether-hydroquinone adducts as primary molecular products. The subsequent chemistry of these products is examined in terms of enzymic reduction, autoxidation, cross-oxidation, disproportionation, and free radical interactions. The detailed chemical mechanisms by which quinoid compounds exert cytotoxic, mutagenic and carcinogenic effects are considered individually in relation to redox cycling, alterations of thiol balance and Ca++ homeostasis, and covalent binding.     

Motility characteristics of boar spermatozoa after addition of prostaglandin F2alpha

Addition of prostaglandin F2alpha (PGF2alpha) to extended boar semen has been shown to slightly increase reproductive parameters in sows such as the conception rate and the total number of piglets born alive. The mechanisms by which PGF2alpha affect these parameters have not yet been elucidated, but it is possible that the sperm transport after insemination is increased. This study investigated whether the sperm motility from 20 Piétrain boars improved when PGF2alpha (Dinolytic; 5 mg PGF2alpha/ml) was added to diluted semen. Different amounts of PGF2alpha (0, 0.5, 1 and 2 ml/100 ml) were tested and the motility was evaluated immediately after addition of PGF2alpha, after 30 min, 2 h, and 24 h. Two computer-assisted semen analysis (CASA) systems, namely the Sperm Quality Analyzer (SQA-IIC) and the Hamilton Thorne (HTR Ceros 12.1) were used to assess the motility parameters. With the SQA-IIC, sperm motility index values of the treated groups were only slightly higher (P>0.05) compared to the negative control group. The different motility parameters measured with the HTR Ceros 12.1 were similar between the treatment groups, except for beat cross frequency, which was higher in the control group (1.5-5%; P<0.001). This study documented that the addition of 2.5, 5 or 10 mg PGF2alpha to 100 ml diluted boar sperm does not increase any sperm motility parameter. Further research is necessary to elucidate mechanisms by which PGF2alpha in diluted semen may improve the reproductive performance in swine farms.     

Structure-activity characterization of sulfide:quinone oxidoreductase variants

Sulfide:quinone oxidoreductase (SQR) is a peripheral membrane protein that catalyzes the oxidation of sulfide species to elemental sulfur. The enzymatic reaction proceeds in two steps. The electrons from sulfides are transferred first to the enzyme cofactor, FAD, which, in turn, passes them onto the quinone pool in the membrane. Several wild-type SQR structures have been reported recently. However, the enzymatic mechanism of SQR has not been fully delineated. In order to understand the role of the catalytically essential residues in the enzymatic mechanism of SQR we produced a number of variants of the conserved residues in the catalytic site including the cysteine triad of SQR from the acidophilic, chemolithotrophic bacterium Acidithiobacillus ferrooxidans. These were structurally characterized and their activities for each reaction step were determined. In addition, the crystal structures of the wild-type SQR with sodium selenide and gold(I) cyanide have been determined. Previously we proposed a mechanism for the reduction of sulfides to elemental sulfur involving nucleophilic attack of Cys356 on C(4A) atom of FAD. Here we also consider an alternative anionic radical mechanism by direct electron transfer from Cys356 to the isoalloxazine ring of FAD.     

Subcloning using simplified adaptor addition.

A simplified procedure for the addition of synthetic oligonucleotide adaptors to subclone DNA fragments with incompatible ends is presented. An organophosphate degradation gene on a PstI fragment was cloned into the HindIII site of the fungal vector pH1S. The opd gene specifies parathion hydrolase and was first isolated from a Flavobacterium sp. The gene was present in 12% of the plasmids recovered and was inserted in either direction with similar frequencies: 53% with the opd start codon distal to the single SalI site of pH1S and 47% in the other orientation. All enzymatic steps were carried out in a single microconcentrator eliminating DNA loss through manipulation and transfer. Normally, during adaptor or linker addition, a larger number of oligonucleotides are attached at each end of the insert DNA and must be removed before cloning. The need for enzymatic digestion to remove excess adaptors was avoided. Traditional methods have utilized phenol/chloroform extraction, ethanol precipitation, gel filtration chromatography, spermine precipitation, or preparative gel electrophoresis. Eliminating these steps resulted in a simpler, more reliable procedure.     

Costimulation of soil glycosidase activity and soil respiration by nitrogen addition

Unprecedented levels of nitrogen (N) have been deposited in ecosystems over the past century, which is expected to have cascading effects on microbially mediated soil respiration (SR). Extracellular enzymes play critical roles on the degradation of soil organic matter, and measurements of their activities are potentially useful indicators of SR. The links between soil extracellular enzymatic activities (EEAs) and SR under N addition, however, have not been established. We therefore conducted a meta‐analysis from 62 publications to synthesize the responses of soil EEAs and SR to elevated N. Nitrogen addition significantly increased glycosidase activity (GA) by 13.0%, α‐1,4‐glucosidase (AG) by 19.6%, β‐1,4‐glucosidase (BG) by 11.1%, β‐1,4‐xylosidase (BX) by 21.9% and β‐D‐cellobiosidase (CBH) by 12.6%. Increases in GA were more evident for long duration, high rate, organic and mixed N addition (combination of organic and inorganic N addition), as well as for studies from farmland. The response ratios (RRs) of GA were positively correlated with the SR‐RRs, even when evaluated individually for AG, BG, BX and CBH. This positive correlation between GA‐RR and SR‐RR was maintained for most types of vegetation and soil as well as for different methods of N addition. Our results provide the first evidence that GA is linked to SR under N addition over a range of ecosystems and highlight the need for further studies on the response of other soil EEAs to various global change factors and their implications for ecosystem functions.