Genetic and biochemical evidence for the involvement of a molybdenum-dependent enzyme in one of the selenite reduction pathways of Rhodobacter sphaeroides f. sp. denitrificans IL106

Selenite bioreduction by a consortium of halophilic/halotolerant bacteria and/or yeasts in saline media

Selenium oxyanions are released into environments by natural and anthropogenic activities and are present in agricultural and glass manufacturing wastewater in several locations worldwide. Excessive amounts of this metalloid have adverse effects on the health of living organisms. Halophilic and halotolerant microorganisms were selected for selenium oxyanions remediation due to presence of significant amount of salt in selenium-containing wastewater. Effects of aeration, carbon sources, competitive electron acceptors, and reductase inhibitors were investigated on SeO₃^2- bio-removal. Additionally, NO₃^--containing wastewater were exploited to investigate SeO₃^2- remediation in synthetic agricultural effluents. The results showed that the SeO₃^2- removal extent is maximum in aerobic conditions with succinate as a carbon source. SO₄^2- and PO₄^3- do not significantly interfere with SeO₃^2- reduction, while WO₄^2- and TeO₃^2- decrease the SeO₃^2- removal percentage (up to 35 and 37%, respectively). Furthermore, NO₃^- had an adverse effect on SeO₃^2- biotransformation by our consortia. All consortia reduced SeO₃^2- in synthetic agricultural wastewaters with a 45-53% removal within 120 h. This study suggests that consortia of halophilic/halotolerant bacteria and yeasts could be applied to treat SeO₃^2--contaminated drainage water. In addition, sulphates, and phosphates do not interfere with selenite bioreduction by these consortia, which makes them suitable candidates for the bioremediation of selenium-containing wastewater.

TRAP transporter TakP: a key player in the resistance against selenite-induced oxidative stress in Rhodobacter sphaeroides

Almost one-third of all proteins require metal ions as an essential component in key biological processes and approximately half of all enzymes are associated with one or more metal ions. The naturally occurring selenium is very toxic at higher levels, but few bacteria can reduce it into the less toxic insoluble elemental selenium. Selenium is required for the synthesis of selenocysteine, an essential residue involved in the active sites of various enzymes. The purple non-sulphur bacteria, Rhodobacter sphaeroidesis demonstrated for its selenite reduction capacity. The exact mechanism of selenite toxicity is unknown but it reacts with glutathione to form selenodiglutathione, producing the highly toxic compounds namely, H₂O₂and O₂^-. A R. sphaeroidesstrain with mutated takP gene, a member of the TRAP (tripartite ATP-independent periplasmic) family of transporter, was reported to be showing more resistance towards selenite in the growth medium but the reason for the resistance is unknown. TRAP transporters are the best-studied family of substrate-binding protein and in our previous study it was confirmed that the gene takP in R. sphaeroides is down-regulated by a small non-coding RNA SorY, providing more resistance to the bacterium against the oxidative stress. By comparative growth analysis and sensitivity assays in the presence of 2 mM selenite, it was observed that the SorY knockout strain is more sensitive to selenite while overexpression of the sRNA conferred more resistance to the bacterium like the takP mutant strain. TakP is involved in the import of malate into the cell, which under oxidative stress needs to be down-regulated to limit malate flux into the cell. Limited malate flux leads to metabolic rearrangements in the cell to avoid excessive generation of prooxidant NADH and facilitate constant generation of antioxidant NADPH. In the presence and absence of selenite, a drastic increase in the NADPH and decrease in the NADH levels are reported respectively. Accumulation of metallic selenium in the cytoplasm was detected via atomic absorption spectrophotometer and our analysis clearly demonstrated the presence of more selenium in the electron micrographs of the SorY knockout strain compared to the takP mutant grown under dark semi-aerobic growth conditions in the presence of selenite. Hence based on our analysis, it is confirmed that lack of TakP transporter led to reduced selenite influx into the cytoplasm, relieving cells with limited generation of ROS, eventually exhibiting more resistance against selenite-induced oxidative stress.

Reduction of Protein Bound Methionine Sulfoxide by a Periplasmic Dimethyl Sulfoxide Reductase

In proteins, methionine (Met) can be oxidized into Met sulfoxide (MetO). The ubiquitous methionine sulfoxide reductases (Msr) A and B are thiol-oxidoreductases reducing MetO. Reversible Met oxidation has a wide range of consequences, from protection against oxidative stress to fine-tuned regulation of protein functions. Bacteria distinguish themselves by the production of molybdenum-containing enzymes reducing MetO, such as the periplasmic MsrP which protects proteins during acute oxidative stress. The versatile dimethyl sulfoxide (DMSO) reductases were shown to reduce the free amino acid MetO, but their ability to reduce MetO within proteins was never evaluated. Here, using model oxidized proteins and peptides, enzymatic and mass spectrometry approaches, we showed that the Rhodobacter sphaeroides periplasmic DorA-type DMSO reductase reduces protein bound MetO as efficiently as the free amino acid L-MetO and with catalytic values in the range of those described for the canonical Msrs. The identification of this fourth type of enzyme able to reduce MetO in proteins, conserved across proteobacteria and actinobacteria, suggests that organisms employ enzymatic systems yet undiscovered to regulate protein oxidation states.

Enrichment of Denitrifying Bacterial Community Using Nitrite as an Electron Acceptor for Nitrogen Removal from Wastewater

This work aimed to enrich a denitrifying bacterial community for economical denitrification via nitrite to provide the basic objects for enhancing nitrogen removal from wastewater. A sequencing batch reactor (SBR) with continuous nitrite and acetate feeding was operated by reasonably adjusting the supply rate based on the reaction rate, and at a temperature of 20 ± 2 °C, pH of 7.5 ± 0.2, and dissolved oxygen (DO) of 0 mg/L. The results revealed that the expected nitrite concentration can be achieved during the whole anoxic reaction period. The nitrite denitrification rate of nitrogen removal from synthetic wastewater gradually increased from approximately 10 mg/(L h) to 275.35 mg/(L h) over 12 days (the specific rate increased from 3.83 mg/(g h) to 51.80 mg/(g h)). Correspondingly, the chemical oxygen demand/nitrogen (COD/N) ratio of reaction decreased from 7.9 to 2.7. Both nitrite and nitrate can be used as electron acceptors for denitrification. The mechanism of this operational mode was determined via material balance analysis of substrates in a typical cycle. High-throughput sequencing showed that the main bacterial community was related to denitrification, which accounted for 84.26% in the cultivated sludge, and was significantly higher than the 2.16% in the seed sludge.

Morphology-tunable tellurium nanomaterials produced by the tellurite-reducing bacterium Lysinibacillus sp. ZYM-1

Although tellurite is highly toxic to organisms, elemental tellurium nanomaterials (TeNMs) have many uses. The microbe-mediated reduction of tellurite to Te(0) has been shown to be a green and cost-effective approach for turning waste into wealth. However, it is difficult to tune the morphology of biogenic nanomaterials. In this study, a series of experiments was conducted to investigate the factors influencing tellurite reduction by the tellurite-reducing bacterium Lysinibacillus sp. ZYM-1, including pH, tellurite concentration, temperature, and heavy metal ions. The optimal removal efficiency of tellurite was respectively achieved at pH 8, 0.5 mM tellurite, and 40 °C. All of the tested metal ions retarded the reduction of tellurite, especially Cd²⁺ and Co²⁺, which completely inhibited its reduction. Further characterization of the biogenic TeNMs indicated that their morphology could be tuned by the tellurite concentration, pH, temperature, and organic solvents used. Regular Te nanosheets were produced using 5 mM tellurite. The TeNMs were primarily synthesized in the cell membrane. Hexagonal Te nanoplates, nanorods, nanoflowers, and nanobranches were synthesized when combining membrane fractions with tellurite and NADH. The diverse morphologies are assumed to be induced by the synergy between the reduction kinetics and the protein structure. Therefore, this study confirmed that the bacterium can tune the morphology of TeNMs, broadening the potential application of biogenic TeNMs.

Pseudomonas seleniipraecipitans proteins potentially involved in selenite reduction

Pseudomonas seleniipraecipitans grows in the presence of high levels of selenite and selenate and reduces both oxyanions to elemental selenium (Se(0)), a property that may make P. seleniipraecipitans useful as an inoculant for biobarriers designed to remove selenite or selenate from ground or surface waters. An earlier study showed that P. seleniipraecipitans nitrate reductase reduced selenate to Se(0), but failed to identify the protein(s) involved in selenite reduction. This study used ammonium sulfate precipitation, hydrophobic interaction chromatography, and native PAGE to isolate two electrophoretic gel regions, identified as bands A and B that showed selenite-reductase-activity. Proteomics was used to identify the proteins present in those regions. Glutathione reductase (GR) was detected in the A-band; based on this information, Saccharomyces cerevisiae GR, obtained from a commercial source, was evaluated and found to have selenite-reductase-activity, confirming that GR can reduce selenite to Se(0). Proteomics was also used to detect the proteins present in the B-band and thioredoxin reductase (ThxR) was detected as a B-band protein; based on this information, E. coli ThxR, obtained from a commercial source, was evaluated and found to have selenite-reductase-activity, confirming that ThxR can reduce selenite to elemental selenium. Thus, evidence presented in this study shows that S. cerevisiae GR and E. coli ThxR can reduce SeO3 (2-) to Se(0) and strongly suggests that P. seleniipraecipitans GR and ThxR can also reduce SeO3 (2-) to Se(0).

Detrimental effect of the 6 His C-terminal tag on YedY enzymatic activity and influence of the TAT signal sequence on YedY synthesis

Background

YedY, a molybdoenzyme belonging to the sulfite oxidase family, is found in most Gram-negative bacteria. It contains a twin-arginine signal sequence that is cleaved after its translocation into the periplasm. Despite a weak reductase activity with substrates such as dimethyl sulfoxide or trimethylamine N-oxide, its natural substrate and its role in the cell remain unknown. Although sequence conservation of the YedY family displays a strictly conserved hydrophobic C-terminal residue, all known studies on Escherichia coli YedY have been performed with an enzyme containing a 6 histidine-tag at the C-terminus which could hamper enzyme activity.

Results

In this study, we demonstrate that the tag fused to the C-terminus of Rhodobacter sphaeroides YedY is detrimental to the enzyme’s reductase activity and results in an eight-fold decrease in catalytic efficiency. Nonetheless this C-terminal tag does not influence the properties of the molybdenum active site, as assayed by EPR spectroscopy. When a cleavable His-tag was fused to the N-terminus of the mature enzyme in the absence of the signal sequence, YedY was expressed and folded with its cofactor. However, when the signal sequence was added upstream of the N-ter tag, the amount of enzyme produced was approximately ten-fold higher.

Conclusion

Our study thus underscores the risk of using a C-terminus tagged enzyme while studying YedY, and presents an alternative strategy to express signal sequence-containing enzymes with an N-terminal tag. It brings new insights into molybdoenzyme maturation in R. sphaeroides showing that for some enzymes, maturation can occur in the absence of the signal sequence but that its presence is required for high expression of active enzyme.

A Rhizobium selenitireducens protein showing selenite reductase activity

Biobarriers remove, via precipitation, the metalloid selenite (SeO₃⁻²) from groundwater; a process that involves the biological reduction of soluble SeO₃⁻² to insoluble elemental red selenium (Se⁰). The enzymes associated with this reduction process are poorly understood. In Rhizobium selenitireducens at least two enzymes are potentially involved; one, a nitrite reductase reduces SeO₃⁻² to Se⁰ but another protein may also be involved which is investigated in this study. Proteins from R. selenitireducens cells were precipitated with ammonium sulfate and run on native electrophoresis gels. When these gels were incubated with NADH and SeO₃⁻² a band of precipitated Se⁰ developed signifying the presence of a SeO₃⁻² reducing protein. Bands were cut from the gel and analyzed for peptides via LCMSMS. The amino acid sequences associated with the bands indicated the presence of an NADH:flavin oxidoreductase that resembles YP_001326930 from Sinorhizobium medicae. The protein is part of a protein family termed old-yellow-enzymes (OYE) that contain a flavin binding domain. OYE enzymes are often involved in protecting cells from oxidative stress and, due in part to an active site that has a highly accessible binding pocket, are generally active on a wide range of substrates. This report is the first of an OYE enzyme being involved in SeO₃⁻² reduction.

The bacterial response to the chalcogen metalloids Se and Te

Microbial metabolism of inorganics has been the subject of interest since the 1970s when it was recognized that bacteria are involved in the transformation of metal compounds in the environment. This area of research is generally referred to as bioinorganic chemistry or microbial biogeochemistry. Here, we overview the way the chalcogen metalloids Se and Te interact with bacteria. As a topic of considerable interest for basic and applied research, bacterial processing of tellurium and selenium oxyanions has been reviewed a few times over the past 15 years. Oddly, this is the first time these compounds have been considered together and their similarities and differences highlighted. Another aspect touched on for the first time by this review is the bacterial response in cell-cell or cell-surface aggregates (biofilms) against the metalloid oxyanions. Finally, in this review we have attempted to rationalize the considerable amount of literature available on bacterial resistance to the toxic metalloids tellurite and selenite.

Effects of temperature and dissolved oxygen on Se(IV) removal and Se(0) precipitation by Shewanella sp. HN-41

Facultative anaerobic Shewanella sp. strain HN-41 was able to utilize selenite (Se(IV)) as a sole electron acceptor for respiration in anaerobic condition, resulting in reduction of Se(IV) and then precipitation of elemental Se nano-sized spherical particles, which were identified using energy-dispersive X-ray spectroscopy and X-ray absorption near-edge structure spectroscopy. When the effects on Se(IV) reduction to elemental Se were studied by varying incubation temperatures and dissolved oxygen contents, Se(IV) reduction occurred more actively with higher removal rate of Se(IV) in aqueous phase and well-shaped spherical Se(0) nanoparticles were formed from the incubations under N(2) (100%) or N(2):O(2) (80%:20%) at 30 degrees C with average diameter values of 181+/-40 nm and 164+/-24 nm, respectively, while relatively less amounts of irregular-shaped Se(0) nanoparticles were produced with negligible amount of Se(IV) reduction and removal under 100% of O(2). The Se particle size distributions based on scanning electron microscopy also showed a general tendency towards decreased Se particle size as oxygen content increased, whereas the particle size seemed uncorrelated to the change in the incubation temperature. These results also suggest that the size-controlled biological Se(0) nanospheres production may be achieved simply by changing the culture conditions.

Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding

BACKGROUND

The import of solutes into the bacterial cytoplasm involves several types of membrane transporters, which may be driven by ATP hydrolysis (ABC transporters) or by an ion or H+ electrochemical membrane potential, as in the tripartite ATP-independent periplasmic system (TRAP). In both the ABC and TRAP systems, a specific periplasmic protein from the ESR family (Extracytoplasmic Solute Receptors) is often involved for the recruitment of the solute and its presentation to the membrane complex. In Rhodobacter sphaeroides, TakP (previously named SmoM) is an ESR from a TRAP transporter and binds alpha-keto acids in vitro.

RESULTS

We describe the high-resolution crystal structures of TakP in its unliganded form and as a complex with sodium-pyruvate. The results show a limited "Venus flytrap" conformational change induced by substrate binding. In the liganded structure, a cation (most probably a sodium ion) is present and plays a key role in the association of the pyruvate to the protein. The structure of the binding pocket gives a rationale for the relative affinities of various ligands that were tested from a fluorescence assay. The protein appears to be dimeric in solution and in the crystals, with a helix-swapping structure largely participating in the dimer formation. A 30 A-long water channel buried at the dimer interface connects the two ligand binding cavities of the dimer.

CONCLUSION

The concerted recruitment by TakP of the substrate group with a cation could represent a first step in the coupled transport of both partners, providing the driving force for solute import. Furthermore, the unexpected dimeric structure of TakP suggests a molecular mechanism of solute uptake by the dimeric ESR via a channel that connects the binding sites of the two monomers.