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PubMed1996

Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions.

Methane is oxidized to methanol by the enzyme methane mono-oxygenase (MMO) in methanotrophic bacteria. In previous work, this multicomponent enzyme system has been extensively characterized at the biochemical and molecular level. Copper ions have been shown to irreversibly inhibit MMO activity in vivo and in vitro, but the effect of copper ions on transcription of the genes encoding the soluble (cytoplasmic) MMO (sMMO) has not previously been investigated. To examine more closely the regulation of bacterial methane oxidation and to determine the role of copper in this process, we have investigated transcriptional regulation of the sMMO gene cluster in the methanotrophic bacterium Methylococcus capsulatus (Bath). Using Northern blot analysis and primer extension experiments, it was shown that the six ORFs of the sMMO gene cluster are organized as an operon and the transcripts produced upon expression of this operon have been identified. The synthesis of these transcripts was under control of a single copper-regulated promoter, which is as yet not precisely defined.

Bacterial Proteins↗
PubMed2005

Solubility of methane in water: the significance of the methane-water interaction potential.

The influence of the methane-water interaction potential on the value of the Henry constant obtained from molecular dynamics simulations was investigated. The SPC, SPC/E, MSPC/E, and TIP3P potentials were used to describe water and the OPLS-UA and TraPPE potentials for methane. Nonbonding interactions between unlike atoms were calculated both with one of four mixing rules and with our new methane-water interaction potential. The Henry constants obtained from simulations using any of the mixing rules differed significantly from the experimental ones. Good agreement between simulation and experiment was achieved with the new potential over the whole temperature range.

Journal Article↗
PubMed2000

Differential inhibition in vivo of ammonia monooxygenase, soluble methane monooxygenase and membrane-associated methane monoxygenase by phenylacetylene.

Phenylacetylene was investigated as a differential inhibitor of ammonia monooxygenase (AMO), soluble methane monooxygenase (sMMO) and membrane-associated or particulate methane monooxygenase (pMMO) in vivo. At phenylacetylene concentrations > 1 microM, whole-cell AMO activity in Nitrosomonas europaea was completely inhibited. Phenylacetylene concentrations above 100 microM inhibited more than 90% of sMMO activity in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b. In contrast, activity of pMMO in M. trichosporium OB3b, M. capsulatus Bath, Methylomicrobium album BG8, Methylobacter marinus A45 and Methylomonas strain MN was still measurable at phenylacetylene concentrations up to 1,000 microM. AMO of Nitrosococcus oceanus has more sequence similarity to pMMO than to AMO of N. europaea. Correspondingly, AMO in N. oceanus was also measurable in the presence of 1,000 microM phenylacetylene. Measurement of oxygen uptake indicated that phenylacetylene acted as a specific and mechanistic-based inhibitor of whole-cell sMMO activity; inactivation of sMMO was irreversible, time dependent, first order and required catalytic turnover. Corresponding measurement of oxygen uptake in whole cells of methanotrophs expressing pMMO showed that pMMO activity was inhibited by phenylacetylene, but only if methane was already being oxidized, and then only at much higher concentrations of phenylacetylene and at lower rates compared with sMMO. As phenylacetylene has a high solubility and low volatility, it may prove to be useful for monitoring methanotrophic and nitrifying activity as well as identifying the form of MMO predominantly expressed in situ.

Acetylene↗
PubMed2006

Bis[bis(3,5-dimethylpyrazol-1-yl)methane]bis(isothiocyanato)cadmium(II) and catena-poly[[di-mu-dicyanamidato-bis{[bis(3,5-dimethylpyrazol-1yl)methane]cadmium(II)}]-di-mu-dicyanamidato].

The Cd atom in bis[bis(3,5-dimethylpyrazol-1-yl)methane]bis(isothiocyanato)cadmium(II), [Cd(NCS)2(C11H16N4)2], is octahedrally coordinated by four N atoms from two bis(3,5-dimethylpyrazolyl)methane (dmpzm) ligands and two isothiocyanate ligands. The molecule has a crystallographic center of symmetry located at the Cd atom. There are two intramolecular C-H...N interactions, each of which is formed between the methylene group of a dmpzm ligand and the N atom of an isothiocyanate ligand. On the other hand, in catena-poly[[di-mu-dicyanamidato-bis{[bis(3,5-dimethylpyrazol-1-yl)methane]cadmium(II)}]-di-mu-dicyanamidato], [Cd2(C2N3)4(C11H16N4)2]n, each Cd atom is octahedrally coordinated by two N atoms from one dmpzm ligand and four N atoms from four bridging dicyanamide (dca) anions. Two Cd atoms are bridged by a pair of dca anions, forming a dimeric [Cd2(mu-dca)2(dmpzm)2] unit. Another two pairs of dca anions further link this unit with neighboring units to form a brick-wall layer parallel to (100). A C-H...N interaction between the methylene group of one dmpzm ligand in one layer and a coordinating N atom of a dca ligand in an adjacent layer completes a three-dimensional network.

Journal Article↗
PubMed2002

Soluble methane monooxygenase: activation of dioxygen and methane.

The mechanisms by which soluble methane monooxygenase uses dioxygen to convert methane selectively to methanol have come into sharp focus. Diverse techniques have clarified subtle details about each step in the reaction, from binding and activating dioxygen, to hydroxylation of alkanes and other substrates, to the electron transfer events required to complete the catalytic cycle.

Alkanes↗
PubMed1996

Large kinetic isotope effects in methane oxidation catalyzed by methane monooxygenase: evidence for C-H bond cleavage in a reaction cycle intermediate.

The reduced hydroxylase component (MMOH) of soluble methane monooxygenase (MMO) from Methylosinus trichosporium OB3b reacts with O2 and CH4 to produce CH3OH and H2O in a single-turnover reaction. Transient kinetic analysis of this reaction has revealed at least five and probably six intermediates during the turnover [Lee, S.-K., Nesheim, J. C., & Lipscomb, J. D. (1993) J. Biol. Chem. 268, 21569-21577; Liu, Y., Nesheim, J. C., Lee, S.-K., & Lipscomb, J. D. (1995) J. Biol. Chem. 270, 24662-24665]. One intermediate, termed compound Q, reacts with CH4 to yield enzyme-bound product. It is shown here that the deuterium kinetic isotope effect (KIE) for the reaction of compound Q with CH4 is 50-100, which is one of the largest effects observed to date. The rate constants for the reactions of the deuterated homologs of methane decrease monotonically as the deuterium content increases, suggesting that a large primary isotope effect dominates. The KIEs determined by analyzing the products after a single turnover have the following values: 1:1 CH4:CD4 (19); CD3H (12); CD2H2 (9); and CH3D (4). The KIE values determined by directly observing the reactive intermediate and by monitoring product ratios are all large, consistent with complete C-H bond breaking in the oxygenation step of the reaction. However, the differences in the KIE values determined by these two methods suggest that the reaction is more complex than currently proposed. A modified mechanism introducing the possibility of hydrogen-atom reabstraction by an intermediate methyl radical is proposed.

Computer Simulation↗
PubMed2003

Comparative oxidation and net emissions of methane and selected non-methane organic compounds in landfill cover soils.

The surface emissions of methane (CH4) and non-methane organic compounds (NMOCs) were determined at two different areas at a French landfill: a permanently covered and fully vegetated area (40 cm coarse sand + 80 cm of loam) and a temporarily covered area (40 cm of coarse sand). The 37 NMOCs quantified in the landfill gas samples included alkanes (C1-C10), alkenes (C1-C4), halogenated hydrocarbons (including (H)CFCs), and aromatic hydrocarbons. Both positive and negative CH4 fluxes ranging from -0.01 to 0.008 g m(-2) d(-1) were measured from the permanently covered cell. However, high spatial variation was observed, and a hot spot with a high flux (10 g m(-2) d(-1)) was identified. A higher CH4 emission occurred from the temporarily covered cell (CH4 flux of 49.9 g m(-2) d(-1)) as compared to the permanently covered cell. The NMOC fluxes from the permanently covered zone were all very small with both positive and negative fluxes in the order of 10(-7) to 10(-5) g m(-2) d(-1). Higher and mainly positive NMOC fluxes in the order of 10(-5) to 10(-4) g m(-2) d(-1) were obtained from the temporarily covered zone. The lower emission from the permanently covered and fully vegetated cell was attributable to the thicker soil layer, which functions as microbial habitat for methanotrophic bacteria. The NMOC oxidation capacity was investigated in soil microcosms incubated with CH4. Maximal oxidation rates for the halogenated aliphatic compounds varied between 0.06 and 8.56 microg (g of soil)(-1) d(-1). Fully substituted hydrocarbons (tetrachloromethane, perchloroethylene, CFC-11, CFC-12, and CFC-113) were not degraded in the presence of CH4 and O2. Benzene and toluene were rapidly degraded, giving very high maximal oxidation rates (28 and 39 microg (g of soil)(-1) d(-1)). On the basis of the emission measurements and the batch experiments conducted, a general pattern was observed between emissions and biodegradability of various NMOCs. The emissions mainly consisted of compounds that were not degradable or slowly degradable, while an uptake of easily degradable compounds was registered. As an example, perchloroethylene, trichloromethane, CFC-11, and CFC-12 were emitted, while atmospheric consumption of aromatic hydrocarbons and lower chlorinated hydrocarbons such as vinyl chloride, dichloromethane, and chloromethane was observed. This study demonstrates that landfill soil covers show a significant potential for CH4 oxidation and co-oxidation of NMOCs. Under certain conditions, landfills may even function as sinks for CH4 and selected NMOCs, like aromatic hydrocarbons and lower chlorinated compounds.

Air Pollution↗
PubMed2002

Reactions of methane monooxygenase intermediate Q with derivatized methanes.

The reactivity of intermediate Q of soluble methane monooxygenase from Methylococcus capsulatus (Bath) with a series of derivatized methanes of general formula CH3-R, where R = CN, NO2, and OH, and their deuterated analogues is described. Despite relatively slow reactions, significant kinetic isotope effects, KIEs, are observed in reactions with acetonitrile and nitromethane; however, none is obtained with methanol. In addition, evidence of a substrate-binding step that occurs prior to substrate oxidation is observed.

Kinetics↗
PubMed1979

A comparison of the substrate and electron-donor specificities of the methane mono-oxygenases from three strains of methane-oxidizing bacteria.

1. Methane mono-oxygenase from Methylosinus trichosporium has the same broad substrate specificity as the analogous enzyme from Methylococcus capsulatus (Bath); the enzyme from Methylomonas methanica is more specific. 2. Contrary to previous reports, NAD(P)H and not ascorbate is the required electron donor for the enzyme from Methylosinus trichosporium. 3. It is concluded that these three bacteria contain similar methane mono-oxygenases.

Methane↗
PubMed1996

[Synthesis of polyfunctional bridging agent-tetrakis (omega-hydroxyproxymethyl) methane and tri (hydroxyproxymethyl) amino methane].

In order to look for the polyfunctional bridging agent. Tetrakis (omega-hydroxyproxymethyl) methane (3) and Tri (omega-hydroxyproxymethyl) aminomethane (4) were prepared from pentaerythritol and trihydroxymethylamino methane respectly. Nine derivatives (5-13) of compounds (3) and (4) were synthesized. The structures of all new compounds (5-13, 15) were confirmed by IR, 1H-NMR and elemental analysis.

Bridged-Ring Compounds↗
PubMedDate not supplied

Heterologous expression of soluble methane monooxygenase genes in methanotrophs containing only particulate methane monooxygenase.

The methanotrophs Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b contain particulate methane monooxygenase (pMMO) and soluble methane monooxygenase (sMMO) genes. Other methanotrophs such as Methylomicrobium album BG8 and Methylocystis parvus OBBP contain only pMMO genes. Although molecular genetic techniques are poorly developed in methanotrophs, sMMO genes were expressed in methanotrophs normally containing only pMMO genes. This was achieved by conjugation using broad-host-range plasmids containing the native promoter and sMMO genes from Mc. capsulatus (Bath) and Ms. trichosporium OB3b. sMMO genes derived from Ms. trichosporium OB3b were expressed in an active form in Mcy. parvus OBBP and in Mm. album BG8. Therefore, all of the genes required for active sMMO synthesis were contained on the broad-host-range plasmids and were expressed in the heterologous hosts. Constitutive synthesis of pMMO was observed in Mm. album BG8 when grown at high and low copper-to-biomass ratios, while transcription of the recombinant sMMO genes was only observed under growth conditions of low copper-to-biomass ratios. Therefore, the regulatory protein(s) for sMMO synthesis was also present on the plasmid used, or the heterologous host contained a regulatory system for sMMO. Expression of sMMO genes in methanotrophs containing only pMMO will assist further investigations on the expression and regulation of MMO genes in methanotrophs.

Cloning, Molecular↗
PubMed2000

A spectroscopic and magnetic study of complexes of bis(2-benzothiazolyl)methanate and bis(2-benzoxazolyl)methanate with Co(II), Ni(II), Cu(II) and Zn(II).

The co-ordination geometry of the complexes M(bbtm)2 and M(bbom)2 (M: Co, Ni, Cu, Zn; bbtm, bis(2-benzothiazolyl)methanate; bbom, bis(2-benzoxazolyl)methanate) are discussed on the basis of their IR, Raman, resonance Raman, electronic and ESR spectra. Compounds of Ni, Co, Zn with both ligands and Cu(bbom)2 resulted to have a distorted tetrahedral geometry. The distortion towards a square planar geometry is more marked for the M(bbtm)2 series than for the M(bbom)2 one. It has been impossible to suggest a co-ordination geometry for Cu(bbtm)2, that probably has a polymeric structure.

Benzoxazoles↗
PubMed2003

Bis(2,5-dimethoxy-4-methylphenyl)methane and bis(2,5-dimethoxy-3,4,6-trimethylphenyl)methane.

Bis(2,5-dimethoxy-4-methylphenyl)methane, C(19)H(24)O(4), (IIa), was obtained and characterized as a minor product from the reaction of toluhydroquinone dimethyl ether (1,4-dimethoxy-2-methylbenzene) with N-(hydroxymethyl)trifluoroacetamide. Similarly, bis(2,5-dimethoxy-3,4,6-trimethylphenyl)methane, C(23)H(32)O(4), (IIb), was prepared from the corresponding reaction of trimethylhydroquinone dimethyl ether (2,5-dimethoxy-1,3,4-trimethylbenzene). The molecules of (IIa) and (IIb) each lie on a twofold axis passing through the methylene group. The dihedral angle between the planar phenyl rings is 73.4 (1) degrees in (IIa) and 77.9 (1) degrees in (IIb). The external bond angles around the bridging methylene group are 116.6 (2) and 117.3 (2) degrees for (IIa) and (IIb), respectively. In (IIa), the methoxy substituents lie in the plane of the ring and are conjugated with the aromatic system, whereas in (IIb), they are almost perpendicular to the phenyl ring and are positioned on opposite sides.

Anisoles↗
PubMed1997

Direct evidence for a soluble methane monooxygenase from type I methanotrophic bacteria: purification and properties of a soluble methane monooxygenase from Methylomonas sp. GYJ3.

The hydroxylase and reductase components of a soluble methane monooxygenase from type I methanotrophs--Methylomonas sp. GYJ3--were purified by a multiple-step LC procedure. The hydroxylase (approximately 240 kDa, determined by an HPLC-size exclusion chromatography method) has three subunits with molecular masses of 56, 43, and 27 kDa, suggesting that the enzyme has an (alphabeta gamma)2 subunit structure. The HPLC method was developed to purify the hydroxylase component, and the purified protein has a specific activity of 541 nmol propene oxide x mg(-1) protein x min(-1), which is two times the specific activity of the protein purified by the two-step LC procedure. The iron content in the hydroxylase purified by the two-step LC procedure is 2.1 mol of Fe per mole of protein, but the iron content in the protein by the HPLC procedure is 3.78 mol of Fe per mole of protein. The diversity of iron contents in this protein is due mainly to the use of different purification methods. The reductase has a molecular mass of 42 kDa. The UV-VIS spectrum of the protein is similar to that of proteins from other methanotrophs, suggesting that the protein contains a FAD cofactor and a [2Fe-2S] center. The partially purified component B stimulated the MMO activity of the hydroxylase and reductase system by 40-fold.

Chromatography, High Pressure Liquid↗
PubMed1995

The mechanism of methane and dioxygen activation in the catalytic cycle of methane monooxygenase.

The binuclear structure of the active center of methane monooxygenase plays a determining role in dioxygen activation and in selectivity and specificity of alkane oxidation with this enzyme. A new mechanism is suggested for binding and activation of O2, which involves side-on binding of O2-(2) to iron atoms followed by its conversion to the bis-mu-oxo complex considered as an alternative of ferryl in CH4 activation. This mechanism results in the sequence of the cleavage of the O-O bond of peroxide O/O2-instead of the opposite sequence O2-/O, which takes place in the case of heme monooxygenase cytochrome P-450. Therefore, in this case there is no necessity of the charge relay system [N.B. Gerber and S.G. Sligar, J. Am. Chem. Soc. 114 (1992) 8742] for the transformation of O2 to an active intermediate. The experiment for checking this hypothesis is suggested.

Iron↗
PubMed2006

Use of a biologically active cover to reduce landfill methane emissions and enhance methane oxidation.

Biologically-active landfill cover soils (biocovers) that serve to minimize CH4 emissions by optimizing CH4 oxidation were investigated at a landfill in Florida, USA. The biocover consisted of 50 cm pre-composted yard or garden waste placed over a 10-15 cm gas distribution layer (crushed glass) over a 40-100 cm interim cover. The biocover cells reduced CH4 emissions by a factor of 10 and doubled the percentage of CH4 oxidation relative to control cells. The thickness and moisture-holding capacity of the biocover resulted in increased retention times for transported CH4. This increased retention of CH4 in the biocover resulted in a higher fraction oxidized. Overall rates between the two covers were similar, about 2g CH4 m(-2)d(-1), but because CH4 entered the biocover from below at a slower rate relative to the soil cover, a higher percentage was oxidized. In part, methane oxidation controlled the net flux of CH4 to the atmosphere. The biocover cells became more effective than the control sites in oxidizing CH4 3 months after their initial placement: the mean percent oxidation for the biocover cells was 41% compared to 14% for the control cells (p<0.001). Following the initial 3 months, we also observed 29 (27%) negative CH4 fluxes and 27 (25%) zero fluxes in the biocover cells but only 6 (6%) negative fluxes and 22 (21%) zero fluxes for the control cells. Negative fluxes indicate uptake of atmospheric CH4. If the zero and negative fluxes are assumed to represent 100% oxidation, then the mean percent oxidation for the biocover and control cells, respectively, for the same period would increase to 64% and 30%.

Air Pollutants↗
PubMed1971

Factors influencing pulmonary methane excretion in man. An indirect method of studying the in situ metabolism of the methane-producing colonic bacteria.

Measurements of pulmonary excretion of methane (CH(4)) were used to obtain information on the CH(4)-producing bacteria in man. Preliminary studies indicated that (a) all CH(4) excreted by man is produced by colonic bacteria, (b) there is no appreciable utilization of CH(4) by man, and (c) breath CH(4) can serve as a relatively accurate indicator of CH(4) production in the intestine. The rate of pulmonary CH(4) excretion varied enormously, ranging from undetectable (<5 x 10(-6) ml/min) to 0.66 ml/minute. In general, the CH(4) excretion rate for subjects was consistently very low (nonproducers) or relatively large (producers). 33.6% of the adult population were producers of CH(4). Whereas diet, age over 10 yr, and sex did not influence the rate of CH(4) production, some familial factor appeared to play an important role. 84% of siblings of CH(4) producers also were producers, while only 18% of the siblings of nonproducers were found to be CH(4) producers. This familial tendency appeared to be determined by early environmental rather than genetic factors. These studies of CH(4) excretion demonstrate that the exposure of individuals to intestinal bacterial metabolites may differ markedly and that these differences may be chronic and determined by familial factors.

ABO Blood-Group System↗