THE ISOLATION AND CHARACTERIZATION OF METHANOMONAS METHANOOXIDANS BROWN AND STRAWINSKI

Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases

Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.

Rates and pathways of CH4 oxidation in ferruginous Lake Matano, Indonesia

This study evaluates rates and pathways of methane (CH₄ ) oxidation and uptake using ¹⁴ C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^-1  day^-1 to 117 μmol L^-1  day^-1 ) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂ ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂ ) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.

Kinetics of CH4 oxidation in mixed culture

Microbial cultures used for methane oxidation experiments were prepared by enriching under a 20 % CH4 atmosphere either leachate extracts from two different landfill sites or a digested sewage sludge. No microbes were axenically isolated, therefore the cultures were mixtures of CH4 oxidising and other aerobic microorganisms. CH4 oxidation experiments were carried out with a batch reactor, whose change in gas volume could be measured. A mixture of air and methane with CH4 concentrations ranging from 5 to 20 % was introduced into the reactor. Methane oxidation rate was expressed as a Monod equation for CH4 and a first order reaction for O2. Maximum oxidation rate (Vmax) resulted 2.1 x 10(-13) to 3.4 x 10(-11) hr(-1) cell(-1), and half saturation constant (KM) was 5.1 x 10(-5) to 6.5 x 10(-4) mol L(-1). The molar ratio of consumed O2 to oxidised CH4 was 1.5-1.8

New type of oxygenase involved in the metabolism of propane and isobutane

Nocardia paraffinicum (Rhodococcus rhodochrous), a hydrocarbon-degrading microorganism, was used in a study of propane and isobutane metabolism. The bacterium was able to utilize propane or isobutane as a sole source of carbon, and oxygen was found to be essential for its metabolism. Gas chromatographic analysis showed that n-propanol was the major compound recovered from the metabolism of propane by resting cells, although trace amounts of isopropanol and acetone were detected. When a mixture of propane and isobutane was used, drastic inhibition (72 to 88%) of hydrocarbon utilization by resting cells occurred. The ratio of hydrocarbon to oxygen consumed was found to be approximately 2:1 during the metabolism of propane or isobutane by resting cells when these substrates were provided individually to the organism. Gas chromatographic-mass spectrometric analysis of products formed from O(2) confirmed that the initial oxidative step in the metabolism of these substrates involved molecular oxygen. The proportion of the alcohol containing O was the same as that of O(2) in the gas mixture. Only a negligible amount of O was detected in the alcohol when H(2)O was incorporated into the system. The observed 2:1 ratio of hydrocarbon to oxygen consumption suggests that the oxygenase in N. paraffinicum, unlike the conventional mono- or dioxygenases, requires two hydrocarbon-binding sites for each of the oxygen-binding sites and is therefore an intermolecular dioxygenase. The newly described oxygenase, which catalyzes the reaction of two molecules of propane with one molecule of oxygen to yield two molecules of a C(3) alcohol, is proposed as the initial oxidation step of the hydrocarbon substrate.

[Effector influence of oxygen-containing C1 compounds in the cultivation of the methanotrophic bacterial strain GB 25]

Addition of oxygen-containing C1-compounds to chemostat cultures of GB 25 increases both the yield of biomass and the specific growth rate. At optimum concentrations the catalytic activity of these compounds increases with increasing growth rates. Their influence on maintenance coefficients and maximum yield coefficients decreases in the order CH3OH greater than CO2 greater than HCOOH greater than HCHO. This result together with spectrophotometric NADH determinations suggests that the NADH pool determines the balance between the assimilatory and oxidative utilization of formaldehyde.

Effect of Nitrogen Source on End Products of Naphthalene Degradation

Soil cultures, enrichment cultures, and pure culture isolates produced substantial quantities of salicylic acid from naphthalene in a mineral salts medium containing NH 4 Cl as the nitrogen source. However, when KNO 3 was substituted for NH 4 Cl, these same cultures failed to accumulate detectable quantities of salicylic acid but did turn the medium yellow. When an isolate identified as a Pseudomonas species was used, viable cell numbers were much greater in the medium containing KNO 3 , but up to 94% of the naphthalene was utilized in both media. After 48 h of incubation in a 0.1% naphthalene-mineral salts medium, the cultures containing NH 4 Cl showed irregular clumped cells, a pH of 4.7, 42 μg of salicylic acid per ml, and the production of 4.4 ml of CO 2 . Under the same conditions, the cultures in the medium containing KNO 3 showed uniform cellular morphology, a pH of 7.3, no salicylic acid, the production of 29.7 ml of CO 2 , and a distinct yellow coloration of the medium. The differences between nitrogen sources could not be accounted for by pH alone since results obtained using buffered media were similar. Growth with NH 4 NO 3 displayed a pattern similar to that obtained when NH 4 Cl was used. The yellow coloration in the medium containing KNO 3 was apparently due to more than one compound, none of which were 1,2-naphthoquinone or acidic in nature, as suggested by other investigators. Further attempts to identify the yellow compounds by high-pressure liquid chromatography, infrared analysis, and gas chromatography-mass spectrometry have been unsuccessful thus far.

Microbial Oxidation of Gaseous Hydrocarbons: Production of Secondary Alcohols from Corresponding n -Alkanes by Methane-Utilizing Bacteria

Over 20 new strains of methane-utilizing bacteria were isolated from lake water and soil samples. Cell suspensions of these and of other known strains of methane-utilizing bacteria oxidized n -alkanes (propane, butane, pentane, hexane) to their corresponding secondary alcohols (2-propanol, 2-butanol, 2-pentanol, 2-hexanol). The product secondary alcohols accumulated extracellularly. The rate of production of secondary alcohols varied with the organism used for oxidation. The average rate of 2-propanol, 2-butanol, 2-pentanol, and 2-hexanol production was 1.5, 1.0, 0.15, and 0.08 μmol/h per 5.0 mg of protein in cell suspensions, respectively. Secondary alcohols were slowly oxidized further to the corresponding methylketones. Primary alcohols and aldehydes were also detected in low amounts (rate of production were 0.05 to 0.08 μmol/h per 5.0 mg of protein in cell suspensions) as products of n -alkane (propane and butane) oxidation. However, primary alcohols and aldehydes were rapidly metabolized further by cell suspensions. Methanol-grown cells of methane-utilizing bacteria did not oxidize n -alkanes to their corresponding secondary alcohols, indicating that the enzymatic system required for oxidation of n -alkanes was induced only during growth on methane. The optimal conditions for in vivo secondary alcohol formation from n -alkanes were investigated in Methylosinus sp. (CRL-15). The rate of 2-propanol and 2-butanol production was linear for the 40-min incubation period and increased directly with cell protein concentration up to 12 mg/ml. The optimal temperature and pH for the production of 2-propanol and 2-butanol were 40°C and pH 7.0. Metalchelating agents inhibited the production of secondary alcohols. The activities for the hydroxylation of n -alkanes in various methylotrophic bacteria were localized in the cell-free particulate fractions precipitated by centrifugation between 10,000 and 40,000 × g . Both oxygen and reduced nicotinamide adenine dinucleotide were required for hydroxylation activity. The metal-chelating agents inhibited hydroxylation of n -alkanes by the particulate fraction, indicating the involvement of a metal-containing enzyme system in the oxidation of n -alkanes. The production of 2-propanol from the corresponding n -alkane by the particulate fraction was inhibited in the presence of methane, suggesting that the subterminal hydroxylation of n -alkanes may be catalyzed by methane monooxygenase.

(1-14C) acetate assimilation by obligate methylotrophs, Pseudomonas methanica and Methylosinus trichosporium

The oxidation of one carbon compounds (methane, methanol, formaldehyde, formate) and primary alcohols (ethanol, propanol, butanol) supported the assimilation of [1-14C]acetate by cell suspensions of type I obligate methylotroph, Pseudomonas methanica, Texas strain, and type II obligate methylotroph, Methylosinus trichosporium, strain PG. The amount of oxygen consumed and substrate oxidized correlated with the amount of [1-14C]acetate assimilated during oxidation of C-1 compounds and primary alcohols. Oxidation of methanol, formaldehyde, and primary alcohols in extracts of Pseudomonas methanica, Texas strain, and Methylosinus trichosporium, strain PG, was catalyzed by a phenazine methosulfate linked, ammonium ion dependent methanol dehydrogenase. The oxidation of aldehydes was catalyzed by a phenazine methosulfate linked, ammonium ion independent aldehyde dehydrogenase. Formate was oxidized by a NAD+ linked formate dehydrogenase.

Enzyme engineering and the anatomy of equilibrium technology

To talk about enzyme engineering in a context of global problems might seem easy, because the subject is so dynamic and its ramifications so numerous. One might for instance talk about the industrial use of immobilized enzymes to achieve steroid transformations suitable for large-scale production of drugs reducing fertility, or one could describe the application of the same technique for chopping off side-chains of penicillin and other antibiotics as a first step in the production of new semisynthetic drugs, that certainly have a global impact. Or it would be tempting to review the potential of enzyme engineering for synthesizing physiologically active polypeptides that find use in husbandry or medicine.

Inhibition of dimethyl ether and methane oxidation in Methylococcus capsulatus and Methylosinus trichosporium

Metal-chelating or -binding agents inhibited the oxidation of dimethyl ether and methane, but not methanol, by cell suspensions of Methylococcus capsulatus and Methylosinus trichosporium. Evidence suggests that the involvement of metal-containing enzymatic systems in the initial step of oxidation of dimethyl ether and methane.

Stoichiometry of methane oxidation in the methane-oxidizing strain M 102 under the influence of various CH4/O2 mixtures

In laboratory-scale experiments with growing cells of the obligate methane-oxidizing strain M 102, an overall molar gas turnover ratio of the order given below could be postulated: 1 CH4+1--1.2 O2=0.3 CO2+water. Expectations that the optimal gas mixture of methane and oxygen should lie within the range of this stoichiometric consumption ratio have been verified in fermenter 5 1 batch culture experiments. The optimal range of methane-oxygen mixture, found under the experimental conditions described, is based on the estimated growth parameters as generation and doubling times, yield coefficients related to methane and oxygen, and the efficiency of methane metabolism as indicated in the absolute amounts of CH4, O2, and CO2 turned over. The mentioned stoichiometric relation of 1 CH4:1--1.202 did not change with varying the composition, i.e. the partial pressures of CH4 and O2 introduced as a mixture to the cells. The efficiency of methane oxidation was obviously influenced and decreased markedly when deviating from the broad optimal range of CH4/O2 mixtures. With non-growing cells, on the other hand, the stoichiometric relation showed a considerable shift (1:1.4--1.8 CH4:O2) with a clear tendency towards more O2 consumption. The oxidation potential of growing cells, seems then to have a linear interdependence to the substrate concentrations, i.e. partial pressures.

Some cultural and physiological aspects of methane-utilizing bacteria

A number of different methane-utilizing bacteria are described and compared with isolates of other investigators. The strains can be divided into three groups based on pigmentation, cell morphology and internal membrane structures. The oxidation of hydrocarbons, alcohols, aldehydes, fatty acids, methyl ethers and sugar phosphates by these bacteria was studied. There was much similarity between strains within the same group. Differences between groups as regards oxidative properties could be detected, but these were mainly quantitative and could not be used as taxonomical criteria. In addition, the inhibition of methane oxidation by metabolites and enzyme inhibitors was investigated. Formaldehyde proved to be the most active of the organic compounds tested. Iodoacetic acid inhibited both methane and methanol oxidation at concentrations of 0.03 M or above. Of the inorganic compounds, KCN completely suppressed methane oxidation at 5 times 10(-4) M and to more than 90% at 5 times 10(-5) M.

Isolation and characterization of bacteria that grow on methane and organic compounds as sole sources of carbon and energy

Bacteria capable of growth on methane and a variety of complex organic substrates as sole sources of carbon and energy have been isolated. Conditions used to rigorously establish the purity of the cultures are described. One facultative methylotroph has been studied in detail. This organism has peripherally arranged pairs of intracytoplasmic membranes characteristic of obligate methylotrophs. This isolate apparently utilizes the serine pathway of formaldehyde fixation. The location of methane oxidizers in a dimictic lake indicates that these organisms prefer less than saturating levels of dissolved oxygen. Laboratory experiments confirmed the preference of these organisms for atmospheres containing less oxygen than air.

New pseudomonad utilizing methanol for growth

A bacterium capable of rapid growth on methanol as sole carbon source was isolated and classified as a new pseudomonad. Its doubling time was about 100 min at 32 to 37 C, and it grew well at methanol concentrations up to 2%. The organism was sensitive to phosphate, but reasonable cell densities could be obtained by using pH control. Cell yields of about 31%, based on methanol consumed, were obtained. The amino acid pattern of the protein indicated that the bacterium holds promise as a source of single-cell protein.

Physiological studies of methane and methanol-oxidizing bacteria: oxidation of C-1 compounds by Methylococcus capsulatus

Methylococcus capsulatus grows only on methane or methanol as its sole source of carbon and energy. Some amino acids serve as nitrogen sources and are converted to keto acids which accumulate in the culture medium. Cell suspensions oxidize methane, methanol, formaldehyde, and formate to carbon dioxide. Other primary alcohols are oxidized only to the corresponding aldehydes. Oxidation of formate by cell suspensions is more sensitive to inhibition by cyanide than is the oxidation of other one carbon compounds. This is due to the cyanide sensitivity of a soluble nicotinamide adenine dinucleotide-specific formate dehydrogenase. Oxidation of formaldehyde and methanol is catalyzed by a nonspecific primary alcohol dehydrogenase which is activated by ammonium ions and is independent of pyridine nucleotides. Some comparisons are made with a strain of Pseudomonas methanica.

Oxygenation of methane by methane-grown Pseudomonas methanica and Methanomonas methanooxidans

1. Experimental conditions have been found in which small amounts of methanol (approximately 2.5mm) accumulated when washed cell suspensions of methane-grown Pseudomonas methanica and Methanomonas methanooxidans were incubated with methane+oxygen mixtures in Warburg flasks. 2. The methanol formed could be separated completely from water by fractional distillation through glass helices followed by gas chromatography using 20% polyethylene glycol 400 on a Celite 545 support. 3. By using (18)O-enriched oxygen gas the abundance of (18)O in the methanol formed from oxidation of methane was measured with a Perkin-Elmer 270 combined gas chromatograph/mass spectrometer. The results showed that the oxygen in methanol was derived exclusively from gaseous oxygen in both micro-organisms. 4. Control experiments using [(18)O]water in incubation mixtures confirmed that there was negligible incorporation of the oxygen atom from water into methanol.

Microbial growth on C1 compounds. Uptake of [14C]formaldehyde and [14C]formate by methane-grown Pseudomonas methanica and determination of the hexose labelling pattern after brief incubation with [14C]methanol

1. A study has been made of the incorporation of carbon from [(14)C]formaldehyde and [(14)C]formate by cultures of Pseudomonas methanica growing on methane. 2. The distribution of radioactivity within the non-volatile constituents of the ethanol-soluble fractions of the cells, after incubation with labelled compounds for periods of up to 1min., has been analysed by chromatography and radioautography. 3. Radioactivity was fixed from [(14)C]formaldehyde mainly into the phosphates of the sugars, glucose, fructose, sedoheptulose and allulose. 4. Very little radioactivity was fixed from [(14)C]formate; after 1min. the only products identified were serine and malate. 5. The distribution of radioactivity within the carbon skeleton of glucose, obtained from short-term incubations with [(14)C]methanol of Pseudomonas methanica growing on methane, has been investigated. At the earliest time of sampling over 70% of the radioactivity was located in C-1; as the time increased the radioactivity spread throughout the molecule. 6. The results have been interpreted in terms of a variant of the pentose phosphate cycle, involving the condensation of formaldehyde with C-1 of ribose 5-phosphate to give allulose phosphate.

Microbial growth on C1 compounds. Incorporation of C1 units into allulose phosphate by extracts of Pseudomonas methanica

1. Incubation of cell-free extracts of methane- or methanol-grown Pseudomonas methanica with [(14)C]formaldehyde and d-ribose 5-phosphate leads to incorporation of radioactivity into a non-volatile product, which has the chromatographic properties of a phosphorylated compound. 2. Treatment of this reaction product with a phosphatase, followed by chromatography, shows the presence of two compounds whose chromatographic properties are consistent with their being free sugars. 3. The minor component of the dephosphorylated products has been identified as fructose. The major component has been identified as allulose (psicose) on the basis of co-chromatography, co-crystallization of the derived phenylosazone and dinitrophenylosazone with authentic derivatives of allulose and behaviour towards oxidation with bromine water. 4. It is suggested that the bacterial extracts catalyse the condensation of a C(1) unit identical with, or derived from, formaldehyde with ribose 5-phosphate to give allulose 6-phosphate. 5. Testing of hexose phosphates and pentose phosphates as substrates has so far shown the reaction to be specific for ribose 5-phosphate. 6. The condensation reaction is not catalysed by extracts of methanol-grown Pseudomonas AM1. 7. A variant of the pentose phosphate cycle, involving this condensation reaction, is suggested as an explanation for the net synthesis of C(3) compounds from C(1) units by P. methanica.