Reactions of dimethylsulfoxide reductase in the presence of dimethyl sulfide and the structure of the dimethyl sulfide-modified enzyme

Influence of the ligand-field on EPR parameters of cis- and trans-isomers in MoV systems relevant to molybdenum enzymes: Experimental and density functional theory study

The electron paramagnetic resonance (EPR) investigation of mononuclear cis- and trans-(L1O)MoOCl2 complexes [L1OH = bis(3,5-dimethylpyrazolyl)-3-tert-butyl-2-hydroxy-5-methylphenyl)methane] reveals a significant difference in their spin Hamiltonian parameters which reflect different equatorial and axial ligand fields created by the heteroscorpionate donor atoms. Density functional theory (DFT) was used to calculate the values of principal components and relative orientations of the g and A tensors, and the molecular framework in four pairs of isomeric mononuclear oxo‑molybdenum(V) complexes (cis- and trans-(L1O)MoOCl2, cis,cis- and cis,trans-(L-N2S2)MoOCl [L-N2S2H2 = N,N'-dimethyl-N,N'-bis(mercaptophenyl)ethylenediamine], cis,cis- and cis,trans-(L-N2S2)MoO(SCN), and cis- and trans-[(dt)2MoO(OMe)]2- [dtH2 = 2,3-dimercapto-2-butene]). Scalar relativistic DFT calculations were conducted using three different exchange-correlation functionals. It was found that the use of hybrid exchange-correlation functional with 25% of the Hartree-Fock exchange leads to the best quantitative agreement between theory and experiment. A simplified ligand-field approach was used to analyze the influence of the ligand fields in all cis- and trans-isomers on energies and contributions of molybdenum d-orbital manifold to g and A tensors and relative orientations. Specifically, contributions that originated from the spin-orbit coupling of the dxz, dyz, and dx2-y2 orbitals into the ground state have been discussed. The new findings are discussed in the context of the experimental data of mononuclear molybdoenzyme, DMSO reductase.

The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters

The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.

Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans

BACKGROUND

Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled.

RESULTS

Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans.

CONCLUSIONS

Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels. Video Abstract.

Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation

Dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are widespread in marine environment, and are important participants in the global sulfur cycle. Microbiol oxidation of DMS to DMSO represents a major sink of DMS in marine surface waters. The SAR11 clade and the marine Roseobacter clade (MRC) are the most abundant heterotrophic bacteria in the ocean surface seawater. It has been reported that trimethylamine monooxygenase (Tmm, EC 1.14.13.148) from both MRC and SAR11 bacteria likely oxidizes DMS to generate DMSO. However, the structural basis of DMS oxidation has not been explained. Here, we characterized a Tmm homolog from the SAR11 bacterium Pelagibacter sp. HTCC7211 (Tmm7211). Tmm7211 exhibits DMS oxidation activity in vitro. We further solved the crystal structures of Tmm7211 and Tmm7211 soaked with DMS, and proposed the catalytic mechanism of Tmm7211, which comprises a reductive half-reaction and an oxidative half-reaction. FAD and NADPH molecules are essential for the catalysis of Tmm7211. In the reductive half-reaction, FAD is reduced by NADPH. In the oxidative half-reaction, the reduced FAD reacts with O2 to form the C4a-(hydro)peroxyflavin. The binding of DMS may repel the nicotinamide ring of NADP+, and make NADP+ generate a conformational change, shutting off the substrate entrance and exposing the active C4a-(hydro)peroxyflavin to DMS to complete the oxidation of DMS. The proposed catalytic mechanism of Tmm7211 may be widely adopted by MRC and SAR11 bacteria. This study provides important insight into the conversion of DMS into DMSO in marine bacteria, leading to a better understanding of the global sulfur cycle.

Electrochemically mediated enantioselective reduction of chiral sulfoxides

The respiratory DMSO reductase from Rhodobacter capsulatus catalyzes the reduction of dimethyl sulfoxide to dimethyl sulfide. Herein, we have utilized this Mo enzyme as an enantioselective catalyst to generate optically pure sulfoxides (methyl p-tolyl sulfoxide, methyl phenyl sulfoxide and phenyl vinyl sulfoxide) from racemic starting materials. A hexaaminecobalt coordination compound in its divalent oxidation state was employed as the mediator of electron transfer between the working electrode and DMSO reductase to continually reactivate the enzyme after turnover. In all cases, chiral HPLC analysis of the reaction mixture revealed that the S-sulfoxide was reduced more rapidly leading to enrichment or isolation of the R isomer.

Spectroscopic and electronic structure studies of a dimethyl sulfoxide reductase catalytic intermediate: implications for electron- and atom-transfer reactivity

The electronic structure of a genuine paramagnetic des-oxo Mo(V) catalytic intermediate in the reaction of dimethyl sulfoxide reductase (DMSOR) with (CH(3))(3)NO has been probed by electron paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism (MCD) spectroscopies. EPR spectroscopy reveals rhombic g- and A-tensors that indicate a low-symmetry geometry for this intermediate and a singly occupied molecular orbital that is dominantly metal centered. The excited-state spectroscopic data were interpreted in the context of electronic structure calculations, and this has resulted in a full assignment of the observed MCD and electronic absorption bands, a detailed understanding of the metal-ligand bonding scheme, and an evaluation of the Mo(V) coordination geometry and Mo(V)-S(dithiolene) covalency as it pertains to the stability of the intermediate and electron-transfer regeneration. Finally, the relationship between des-oxo Mo(V) and des-oxo Mo(IV) geometric and electronic structures is discussed relative to the reaction coordinate in members of the DMSOR enzyme family.

Spectroscopic and kinetic studies of Y114F and W116F mutants of Me2SO reductase from Rhodobacter capsulatus

Mutants of the active site residues Trp-116 and Tyr-114 of the molybdenum-containing Me(2)SO reductase from Rhodobacter capsulatus have been examined spectroscopically and kinetically. The Y114F mutant has an increased rate constant for oxygen atom transfer from Me(2)SO to reduced enzyme, the result of lower stability of the E(red).Me(2)SO complex. The absorption spectrum of this species (but not that of either oxidized or reduced enzyme) is significantly perturbed in the mutant relative to wild-type enzyme, consistent with Tyr-114 interacting with bound Me(2)SO. The as-isolated W116F mutant is only five-coordinate, with one of the two equivalents of the pyranopterin cofactor found in the enzyme dissociated from the molybdenum and replaced by a second Mo=O group. Reduction of the mutant with sodium dithionite and reoxidation with Me(2)SO, however, regenerates the long-wavelength absorbance of functional enzyme, although the wavelength maximum is shifted to 670 nm from the 720 nm of wild-type enzyme. This "redox-cycled" mutant exhibits a Me(2)SO reducing activity and overall reaction mechanism similar to that of wild-type enzyme but rapidly reverts to the inactive five-coordinate form in the course of turnover.

Interaction of product analogues with the active site of rhodobacter sphaeroides dimethyl sulfoxide reductase

We report a structural characterization using X-ray absorption spectroscopy of Rhodobacter sphaeroides dimethyl sulfoxide (DMSO) reductase reduced with trimethylarsine and show that this is structurally analogous to the physiologically relevant dimethyl sulfide reduced DMSO reductase. Our data unambiguously indicate that these species should be regarded as formal MoIV species and indicate a classical coordination complex of trimethylarsine oxide, with no special structural distortions. The similarity of the trimethylarsine and dimethyl sulfide complexes suggests, in turn, that the dimethyl sulfide reduced enzyme possesses a classical coordination of DMSO with no special elongation of the S-O bond, as previously suggested.

Photoreactions of p-Quinones with Dimethyl Sulfide and Dimethyl Sulfoxide in Aqueous Acetonitrile†

The effects of dimethyl sulfide (DMS) and dimethyl sulfoxide (DMSO) on the photoreactions of 1,4-benzoquinone (BQ), 1,4-naphthoquinone (NQ), 9,10-anthraquinone (AQ) and several derivatives in acetonitrile/water were studied. The observed triplet state of the quinones is quenched and the rate constant is close to the diffusion-controlled limit for reactions of most quinones with DMS and lower with DMSO. Semiquinone radical anions (Q*-) produced by electron transfer from sulfur to the triplet quinone were detected. For both DMS and DMSO the yield of Q*- is similar, being generally low for BQ and NQ, substantial for AQ and largest for chloranil. The specific quencher concentrations and the effects of quinone structure and redox potentials on the time-resolved photochemical properties are discussed.

Mechanistic Studies of Rhodobacter sphaeroides Me2SO Reductase

Studies of the molybdenum-containing dimethyl sulfoxide reductase from Rhodobacter sphaeroides have yielded new insight into its catalytic mechanism. A series of reductive titrations, performed over the pH range 6-10, reveal that the absorption spectrum of reduced enzyme is highly sensitive to pH. The reaction of reduced enzyme with dimethyl sulfoxide is found to be clearly biphasic throughout the pH range 6-8 with a fast, initial substrate-binding phase and substrate-concentration independent catalytic phase. The intermediate formed at the completion of the fast phase has the characteristic absorption spectrum of the established dimethyl sulfoxide-bound species. Quantitative reductive and oxidative titrations of the enzyme demonstrate that the molybdenum center takes up only two reducing equivalents, implying that the two pyranopterin equivalents of the molybdenum center are not formally redox active. Finally, the visible spectrum associated with the catalytically relevant "high-g split" Mo(V) species has been determined. Spectral deconvolution and EPR quantitation of enzyme-monitored turnover experiments with trimethylamine N-oxide as substrate reveal that no substrate-bound intermediate accumulates and that Mo(V) content remains near unity for the duration of the reaction. Similar experiments with dimethyl sulfoxide show that significant quantities of both the Mo(V) species and the dimethyl sulfoxide-bound complex accumulate during the course of reaction. Accumulation of the substrate-bound complex in the steady-state with dimethyl sulfoxide arises from partial reversal of the physiological reaction in which the accumulating product, dimethyl sulfide, reacts with oxidized enzyme to yield the substrate-bound intermediate, a process that significantly slows turnover.

Odor compounds in waste gas emissions from agricultural operations and food industries

In the last decades, large-scale agricultural operations and food industries have increased. These operations generate numerous types of odors. The reduction of land areas available for isolation of agricultural and food processing industrial operations from the public area and the increase in sensitivity and demand of the general public for a clean and pleasant environment have forced all of these industries to control odor emissions and toxic air pollutants. To develop environmentally sound, sustainable agricultural and food industrial operations, it is necessary to integrate research that focuses on modern analytical techniques and latest sensory technology of measurement and evaluation of odor and pollution, together with a fundamental knowledge of factors that are the basic units contributing to the production of odor and pollutants. Without a clear understanding of what odor is, how to measure it, and where it originates, it will be difficult to control the odor. The present paper reviews the available information regarding odor emissions from agricultural operations and food industries by giving an overview about odor problems, odor detection and quantification, and identifying the sources and the mechanisms that contribute to the odor emissions. Finally, ways of reducing or controlling the odor problem are discussed.

The critical role of tryptophan-116 in the catalytic cycle of dimethylsulfoxide reductase from Rhodobacter capsulatus

In dimethylsulfoxide reductase of Rhodobacter capsulatus tryptophan-116 forms a hydrogen bond with a single oxo ligand bound to the molybdenum ion. Mutation of this residue to phenylalanine affected the UV/visible spectrum of the purified Mo(VI) form of dimethylsulfoxide reductase resulting in the loss of the characteristic transition at 720 nm. Results of steady-state kinetic analysis and electrochemical studies suggest that tryptophan 116 plays a critical role in stabilizing the hexacoordinate monooxo Mo(VI) form of the enzyme and prevents the formation of a dioxo pentacoordinate Mo(VI) species, generated as a consequence of the dissociation of one of the dithiolene ligands of the molybdopterin cofactor from the Mo ion.

Environmental VOSCs--formation and degradation of dimethyl sulfide, methanethiol and related materials

Volatile organic sulfur compounds (VOSCs) play a major role in the global sulfur cycle. Two components, dimethyl sulfide (DMS) and methanethiol (MT) are formed in large amounts by living systems (e.g. algae, bacteria, plants), particularly in marine environments. A major route to DMS is by action of a lyase enzyme on dimethylsulfoniopropionate (DMSP). DMSP has other roles, for instance as an osmoprotectant and cryoprotectant. Demethiolation of DMSP and other materials leads to MT. A major transport process is release of DMS from the oceans to the atmosphere. Oxidation of DMS in the atmosphere by hydroxyl and nitrate radicals produces many degradation products including CO2, COS, dimethyl sulfoxide, dimethyl sulfone, organic oxyacids of sulfur, and sulfate. These materials also have roles in biotic processes and there are complex metabolic interrelationships between some of them. This review emphasizes the chemical reactions of the organic sulfur cycle. For biotic reactions, details of relevant enzymes are provided when possible.

Redox characteristics of the tungsten DMSO reductase ofRhodobacter capsulatus

The dimethylsulfoxide reductase (DMSOR) from Rhodobacter capsulatus is known to retain its three-dimensional structure and enzymatic activity upon substitution of molybdenum, the metal that occurs naturally at the active site, by tungsten. The redox properties of tungsten-substituted DMSOR (W-DMSOR) have been investigated by a dye-mediated reductive titration with the concentration of the W(V) state monitored by EPR spectroscopy. At pH 7.0, E(m)(W(VI)/W(V)) is -194 mV and E(m)(W(V)/W(IV)) is -134 mV. Each E(m) value of W-DMSOR is significantly lower (220 and 334 mV, respectively) than that of the corresponding couple of Mo-DMSOR. These redox potentials are consistent with the ability of Mo-DMSOR to catalyze both the reduction of DMSO to DMS and the back reaction, whereas W-DMSOR is very effective in catalyzing the forward reaction, but shows no ability to catalyze the oxidation of DMS to DMSO.

Small organoselenium molecules. 1. Dimethyl selenoxide: structure, complexation, and gas-phase transformation

For the first time the structural characterization of dimethyl selenoxide coordinated to metal complexes has been performed confirming the Me(2)SeO arrangement assigned by spectroscopic techniques for the molecule in solution and solid state. The structure of Me(2)SeO is trigonal pyramidal with Se-O and Se-C bond lengths of 1.70 and 1.92 A, respectively, and sigma(X-Se-Y) = 301 degrees. As a ligand, dimethyl selenoxide was found to bind to the rhodium centers of various Lewis acidity strengths by using only its oxo functionality in both terminal and bridging fashions. This O-directed coordination preference contrasts with an ambidentate (-S and -O) binding character revealed by dimethyl sulfoxide upon formation of analogous donor-acceptor complexes. The study of dimethyl selenoxide in the gas phase at 135-140 degrees C resulted in a thermal degradation of this molecule. The major decomposition product has been entrapped by a metal complex and identified as dimethyl selenide. The isolation of the coordinated Me(2)Se fragment clearly demonstrates that the Me(2)SeO molecule is less thermally stable than Me(2)SO, which under similar reaction conditions shows no sign of decomposition at temperatures up to 160 degrees C.

Biotin sulfoxide reductase: Tryptophan 90 is required for efficient substrate utilization

Rhodobacter sphaeroides f. sp. denitrificans biotin sulfoxide reductase (BSOR) catalyzes the reduction of d-biotin d-sulfoxide to biotin and contains the molybdopterin guanine dinucleotide (MGD) cofactor as its sole prosthetic group. Comparison of the primary sequences of BSOR and the closely related enzyme dimethyl sulfoxide reductase (DMSOR) indicated a number of conserved residues, including an active-site tryptophan residue (W90), which has been suggested to be involved in hydrogen bonding to the oxo group on the Mo(VI) center in BSOR. Site-directed mutagenesis has been used to replace tryptophan 90 in BSOR with phenylalanine, tyrosine, and alanine residues to examine the role of this residue in catalysis. All three BSOR mutant proteins were purified to homogeneity and contained MGD. The mutant proteins retained very limited activity toward the oxidizing substrates tested, with W90F retaining the most activity (3.4% of wild type). All three W90 mutant proteins exhibited greatly reduced k(cat) values compared to that of the wild-type enzyme, which was accompanied by little change in K(mapp). In addition, the mutant proteins had perturbed visible absorption and circular dichroism spectra suggesting different oxidation states of the Mo center. Purified samples of wild-type BSOR did not exhibit electron paramagnetic resonance (EPR) signals indicating a Mo(VI) center. After redox-cycling, partially reduced samples of wild-type BSOR revealed a proton-split S=1/2 Mo(V) resonance (g(1,2,3)=1.999, 1.981, 1.967; A(1,2,3)=1.40, 1.00, 1.05 mT) analogous to that observed in DMSOR. In contrast, EPR studies of the purified W90 mutant proteins revealed distinct S=1/2 Mo(V) resonances that were resistant to both oxidation and reduction, indicating that the Mo was trapped in the intermediate Mo(V) oxidation state. These results strongly suggest that W90 in BSOR plays a critical role in catalysis by serving as a hydrogen bond donor to the oxo group on the Mo(VI) center.

Probing the electronic structure of [MoOS(4)](-) centers using anionic photoelectron spectroscopy

Using photodetachment photoelectron spectroscopy (PES) in the gas phase, we investigated the electronic structure and chemical bonding of six anionic [Mo(V)O](3+) complexes, [MoOX(4)](-) (where X = Cl (1), SPh (2), and SPh-p-Cl (3)), [MoO(edt)(2)](-) (4), [MoO(bdt)(2)](-) (5), and [MoO(bdtCl(2))(2)](-) (6) (where edt = ethane-1,2-dithiolate, bdt = benzene-1,2-dithiolate, and bdtCl(2) = 3,6-dichlorobenzene-1,2-dithiolate). The gas-phase PES data revealed a wealth of new electronic structure information about the [Mo(V)O](3+) complexes. The energy separations between the highest occupied molecular orbital (HOMO) and HOMO-1 were observed to be dependent on the O-Mo-S-C(alpha) dihedral angles and ligand types, being relatively large for the monodentate ligands, 1.32 eV for Cl and 0.78 eV for SPh and SPhCl, compared to those of the bidentate dithiolate complexes, 0.47 eV for edt and 0.44 eV for bdt and bdtCl(2). The threshold PES feature in all six species is shown to have the same origin and is due to detaching the single unpaired electron in the HOMO, mainly of Mo 4d character. This result is consistent with previous theoretical calculations and is verified by comparison with the PES spectra of two d(0) complexes, [VO(bdt)(2)](-) and [VO(bdtCl(2))(2)](-). The observed PES features are interpreted on the basis of theoretical calculations and previous spectroscopic studies in the condensed phase.