Quantification of coenzymes and related compounds from methanogenic bacteria by high-performance liquid chromatography

Hemoproteins in dissimilatory sulfate- and sulfur-reducing prokaryotes

Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.

Comparison of methane production rate and coenzyme f(420) content of methanogenic consortia in anaerobic granular sludge

The coenzyme F(420) content of granular sludge grown on various substrates and substrate combinations was measured, and the potential of the sludge to form methane (maximum specific methane production rate) from hydrogen, formate, acetate, propionate, and ethanol was determined. The F(420) content varied between 55 nmol g of volatile suspended solids (VSS) for sludge grown on acetate and 796 nmol g of VSS for sludge grown on propionate. The best correlation was found between the F(420) content and the potential activity for methane formation from formate; almost no correlation, however, was found with acetate as the test substrate. The ratio between the potential methanogenic activities (qch(4)) of sludges grown on various substrates and their F(420) content was in general highest for formate (48.2 mumol of CH(4) mumol of F(420) min) and lowest for propionate (6.9 mumol of CH(4) mumol of F(420) min) as test substrates. However, acetate-grown granular sludge with acetate as test substrate showed the highest ratio, namely, 229 mumol of CH(4) mumol of F(420) min. The data presented indicate that the F(420) content of methanogenic consortia can be misleading for the assessment of their potential acetoclastic methanogenic activity.

Purification and characterization of coenzyme F390 synthetase from Methanobacterium thermoautotrophicum (strain delta H)

Coenzyme F390 synthetase catalyzes the formation of 8-hydroxyadenylylated-coenzyme F420 (coenzyme F390-A) from coenzyme F420 and ATP in some methanogenic Archaea. The presence of coenzyme F390 was found when these organisms were exposed to oxygen. To get more insight into the defined function of coenzyme F390, the coenzyme F390 synthetase from Methanobacterium thermoautrophicum was purified from a cell-free extract and its catalytic properties were determined. The synthetase was purified 150-fold to a specific activity of 0.45 mumol.min-1.mg protein-1. The enzyme consisted of one polypeptide of approximately 51 kDa. The isolated enzyme showed a tendency to aggregate into dimers and tetramers upon concentration. Co-elution during purification of GTP-dependent coenzyme F390 synthetase activity suggested that the synthetase is also capable of 8-hydroxyguanylylated-coenzyme F420 (coenzyme F390-G) formation. Initial-velocity measurements of the two-substrate reaction showed that the enzyme kinetics for the coenzyme F390 synthetase reaction proceeded by a ternary-complex mechanism. The coenzyme F390 synthetase displayed a Km for coenzyme F420 of 39 microM and a Km for ATP of 1.7 mM. In contrast to the enzyme in the cell-free extract, the isolated enzyme was active under aerobic and anaerobic conditions. Treatment with air was not required to obtain the enzyme in an active form. However, 1,5-dihydro-coenzyme F420 (coenzyme F420H2) appeared to be a potent competitive inhibitor (Ki 3 microM) with respect to coenzyme F420. The latter findings may explain why the enzyme could only be detected in crude extracts that had been exposed to air, i.e. treatment with air causes the oxidation of reduced coenzyme F420 present in anaerobic extracts. The results of this study are discussed in view of the proposed role for coenzyme F390 in methanogenic metabolism.

Hydrolysis and reduction of factor 390 by cell extracts of Methanobacterium thermoautotrophicum (strain delta H)

Cell extracts of Methanobacterium thermoautotrophicum (strain delta H) were found to perform a hydrogen-dependent reduction of factor 390 (F390), the 8-adenylyl derivative of coenzyme F420. Upon resolution of cell extracts, F390-reducing activity copurified with the coenzyme F420-dependent hydrogenase. This indicates that F390 serves as a substrate of that enzyme. Activity towards F390 was approximately 40-fold lower than that towards coenzyme F420 (0.12 and 5.2 mumol.min-1.mg of protein-1, respectively). In addition, cell extracts catalyzed the hydrolysis of F390 to AMP and coenzyme F420. This hydrolysis required the presence of thiols (6 mM) and much ionic strength (1 M KCl) and was reversibly inhibited by oxygen. The reaction proceeded optimally at pH 8.2 and was Mn dependent. Conditions for F390 hydrolysis in cell extracts are in many respects opposite to those previously described for F390 synthesis.

Purification and characterization of coenzyme F420-dependent 5,10-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum strain delta H

5,10-Methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum strain delta H was purified to homogeneity with nearly complete recovery. The aerobically stable monofunctional enzyme catalyzed the reversible oxidation of 5,10-methylene-5,6,7,8-tetrahydromethanopterin to its 5,10-methenyl derivative. For the reaction a midpoint potential E'0 = - 362 mV was calculated at 60 degrees C. The methanogenic electron carrier coenzyme F420 was strictly required as the co-substrate. The dehydrogenase (Mr 216,000) was purified as an apparent hexamer of six identical 36 kDa subunits. Oxidation of 5,10-methylenetetrahydromethanopterin coupled to coenzyme F420 reduction catalyzed by the dehydrogenase with a turnover number of 2400 S-1 proceeded via a ternary complex mechanism. High concentrations of monovalent cations markedly stimulated the reaction.

Purification and properties of 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri

The 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri was purified 313-fold to a specific activity of 470 mumol min-1 mg-1 at 37 degrees C and pH 7.8. At this stage, the enzyme was pure as judged from polyacrylamide gel electrophoresis. The monofunctional enzyme was oxygen stable, but the presence of a detergent proved to be essential for its stability. Like the cyclohydrolase purified from Methanobacterium thermoautotrophicum (A. A. Dimarco, M. I. Donnelly, and R. S. Wolfe, J. Bacteriol. 168:1372-1377, 1986), the protein showed an apparent Mr of 82,000, and it is composed of two identical subunits as was concluded from nondenaturating and denaturating polyacrylamide gel electrophoresis. The enzymes from M. thermoautotrophicum and M. barkeri markedly differ with respect to the hydrolysis product of 5,10-methenyltetrahydromethanopterin: 5-formyl- and 10-formyltetrahydromethanopterin, respectively. The apparent Km for 5,10-methenyltetrahydromethanopterin was 0.57 mM at 37 degrees C and pH 7.8.

Stimulation of the methylcoenzyme M reduction by uridine-5'-diphospho-sugars in cell-free extracts of Methanobacterium thermoautotrophicum (strain delta H)

The hydrogen-dependent reduction of methylcoenzyme M catalyzed by coenzyme-depleted cell-free extracts of Methanobacterium thermoautotrophicum was stimulated by micromolar concentrations of a UDP-disaccharide present in the organism. The compound was isolated and identified as UDP-1-O-alpha-D-2-acetamido-2-deoxyglucopyranose (UDPGlcpNAc) glycosidically linked to 2-acetamido-2-deoxymannopyranosyluronic acid. Maximal stimulation was observed when both the UDP-disaccharide and mercaptoheptanoylthreonine phosphate were present in the reaction mixtures. The UDP derivative isolated was not specific in its action: other UDP-sugars tested in micromolar concentrations stimulated the methylcoenzyme M reduction to the same extent. The activated sugars presumably substitute for ATP, which is usually required in much higher concentrations to activate the methylcoenzyme M reductase system.

Changes in concentrations of coenzyme F420 analogs during batch growth of Methanosarcina barkeri and Methanosarcina mazei

Coenzyme F420 has been assayed by high-performance liquid chromatography with fluorimetric detection; this permits quantification of individual coenzyme F420 analogs whilst avoiding the inclusion of interfering material. The total intracellular coenzyme F420 content of Methanosarcina barkeri MS cultivated on methanol and on H2-CO2 and of Methanosarcina mazei S-6 cultured on methanol remained relatively constant during batch growth. The most abundant analogs in M. barkeri were coenzymes F420-2 and F420-4, whilst in M. mazei coenzymes F420-2 and F420-3 predominated. Significant changes in the relative proportions of the coenzyme F420 analogs were noted during batch growth, with coenzymes F420-2 and F420-4 showing opposite responses to each other and the same being also true for coenzymes F420-3 and F420-5. This suggests that an enzyme responsible for transferring pairs of glutamic acid residues may be active. The degradation fragment FO was also detected in cells in late exponential and stationary phase. Coenzyme F420 analogs were present in the culture supernatant of both methanogens, in similar proportions to that in the cells, except for FO which was principally located in the supernatant.

Relationship between Methanogenic Cofactor Content and Maximum Specific Methanogenic Activity of Anaerobic Granular Sludges

In this study we investigated whether a relationship exists between the methanogenic activity and the content of specific methanogenic cofactors of granular sludges cultured on different combinations of volatile fatty acids in upflow anaerobic sludge blanket or fluidized-bed reactors. Significant correlations were measured in both cases between the contents of coenzyme F 420 −2 or methanopterin and the maximum specific methanogenic activities on propionate, butyrate, and hydrogen, but not acetate. For both sludges the content of sarcinapterin appeared to be correlated with methanogenic activities on propionate, butyrate, and acetate, but not hydrogen. Similar correlations were measured with regard to the total content of coenzyme F 420 −4 and F 420 −5 in sludges from fluidized-bed reactors. The results indicate that the contents of specific methanogenic cofactors measured in anaerobic granular sludges can be used to estimate the hydrogenotrophic or acetotrophic methanogenic potential of these sludges.

Inorganic pyrophosphate synthesis during methanogenesis from methylcoenzyme M by cell-free extracts of Methanobacterium thermoautotrophicum (strain delta H)

Cell-free extracts of Methanobacterium thermoautotrophicum (strain delta H) were found to contain high concentrations of inorganic pyrophosphate (up to 40 mM). The compound was accumulated by the organism despite high activity of inorganic pyrophosphatase which was found to be present in the cell extracts (1-2 mumol min-1 mg protein-1). This activity was strongly inhibited at [PPi] greater than 1.0 mM. It was demonstrated that PPi synthesis occurred during methylcoenzyme M reduction under hydrogen atmosphere: in the first stage of the reaction for each mole of methane formed one mole of PPi was produced. Inhibition of the methylcoenzyme M reduction by 2-bromoethanesulfonic acid or by high concentrations (greater than 3 microM) of tetrachlorosalicylanilide also inhibited PPi synthesis. In contrast, low concentrations (1.3 microM) of tetrachlorosalicylanilide only inhibited PPi synthesis to the same extent as the methylcoenzyme M reduction was affected. In a later stage of the methylcoenzyme M reduction, PPi synthesis dropped and a second, as yet unidentified, unstable compound was formed. Synthesis of this compound also paralleled methane formation in a stoichiometric way and was affected by the inhibiting substances in a similar way as PPi synthesis.

Relationship of Intracellular Coenzyme F 420 Content to Growth and Metabolic Activity of Methanobacterium bryantii and Methanosarcina barkeri

The use of F 420 as a parameter for growth or metabolic activity of methanogenic bacteria was investigated. Two representative species of methanogens were grown in batch culture: Methanobacterium bryantii (strain M.o.H.G.) on H 2 and CO 2 , and Methanosarcina barkeri (strain Fusaro) on methanol or acetate. The total intracellular content of coenzyme F 420 was followed by high-resolution fluorescence spectroscopy. F 420 concentration in M. bryantii ranged from 1.84 to 3.65 μmol · g of protein −1 ; and in M. barkeri grown with methanol it ranged from 0.84 to 1.54 μmol · g −1 depending on growth conditions. The content of F 420 in M. barkeri was influenced by a factor of 2 depending on the composition of the medium (minimal or complex) and by a factor of 3 to 4 depending on whether methanol or acetate was used as the carbon source. A comparison of F 420 content with protein, cell dry weight, optical density, and specific methane production rate showed that the intracellular content of F 420 approximately followed the increase in biomass in both strains. In contrast, no correlation was found between specific methane production rate and intracellular F 420 content. However, qCH 4 (F 420 ), calculated by dividing the methane production rate by the coenzyme F 420 concentration, almost paralleled qCH 4 (protein). These results suggest that F 420 may be used as a specific parameter for estimating the biomass, but not the metabolic activity, of methanogens; hence qCH 4 (F 420 ) determined in mixed populations with complex carbon substrates must be considered as measure of the actual methanogenic activity and not as a measure of potential activity.

Structure of a methanofuran derivative found in cell extracts of Methanosarcina barkeri

Cell extracts prepared from cells of Methanosarcina barkeri grown on hydrogen and carbon dioxide, acetate, or methanol contain a coenzyme structurally related to methanofuran. This modified coenzyme was highly purified and its structure assigned as 4-[N-(gamma-L-glutamyl-gamma-L-glutamyl-gamma-L-glutamyl-gamma-L-glutamy l)-p- (beta-amino-ethyl)phenoxymethyl]-2-(aminomethyl)furan. The key structural evidence was obtained by high-resolution fast atom bombardment-mass spectrometry and 1H NMR spectroscopy. Quantitative analysis of the hydrolytic fragments of the coenzyme supported the assigned structure. We propose that this coenzyme be called methanofuran-b.

7-Methylpterin and 7-methyllumizine: oxidative degradation products of 7-methyl-substituted pteridines in methanogenic bacteria

7-Methylpterin and 7-methyllumizine were isolated and identified in extracts of methanogenic bacteria which had been extracted in air with ethanol-water. Ethanol-water preparations of cells extracted under nitrogen or hydrogen were devoid of these compounds. Extracts of cells obtained in the presence of air also had an increased amount of a complex arylamine which, on acid hydrolysis, gave 1 mol each of phosphate, 5-(p-aminophenyl)-1,2,3,4-tetrahydroxypentane, and alpha-hydroxyglutaric acid. Gas chromatography-mass spectrometry was used to identify the 5-(p-aminophenyl)-1,2,3,4-tetrahydroxypentane as its tetratrimethylsilyl derivative and the alpha-hydroxyglutaric acid as the n-butyl ester derivative of its gamma-lactone. When exposed to air, extracts of cells prepared in the absence of air produced 6-acetyl-7-methylpterin and 7-methylxanthopterin in addition to 7-methylpterin and 7-methyllumizine. It is concluded that these compounds are derived from the oxidative cleavage of the tetrahydromethanopterin, which is present in these bacteria, by a series of reactions analogous to those known to occur in the oxidative cleavage of tetrahydrofolic acid.

The bioenergetics of methanogenesis

The reduction of CO2 or any other methanogenic substrate to methane serves the same function as the reduction of oxygen, nitrate or sulfate to more reduced products. These exergonic reactions are coupled to the production of usable energy generated through a charge separation and a protonmotive-force-driven ATPase. For the understanding of how methanogens derive energy from C-1 unit reduction one must study the biochemistry of the chemical reactions involved and how these are coupled to the production of a charge separation and subsequent electron transport phosphorylation. Data on methanogenesis by a variety of organisms indicates ubiquitous use of CH3-S-CoM as the final electron acceptor in the production of methane through the methyl CoM reductase and of 5-deazaflavin as a primary source of reducing equivalents. Three known enzymes serve as catalysts in the production of reduced 5-deazaflavin: hydrogenase, formate dehydrogenase and CO dehydrogenase. All three are potential candidates for proton pumps. In the organisms that must oxidize some of their substrate to obtain electrons for the reduction of another portion of the substrate to methane (e.g., those using formate, methanol or acetate), the latter two enzymes may operate in the oxidizing direction. CO2 is the most frequent substrate for methanogenesis but is the only substrate that obligately requires the presence of H2 and hydrogenase. Growth on methanol requires a B12-containing methanol-CoM methyl transferase and does not necessarily need any other methanogenic enzymes besides the methyl-CoM reductase system when hydrogenase is present. When bacteria grow on methanol alone it is not yet clear if they get their reducing equivalents from a reversal of methanogenic enzymes, thus oxidizing methyl groups to CO2. An alternative (since these and acetate-catabolizing methanogens possess cytochrome b) is electron transport and possible proton pumping via a cytochrome-containing electron transport chain. Several of the actual components of the methanogenic pathway from CO2 have been characterized. Methanofuran is apparently the first carbon-carrying cofactor in the pathway, forming carboxy-methanofuran. Formyl-FAF or formyl-methanopterin (YFC, a very rapidly labelled compound during 14C pulse labeling) has been implicated as an obligate intermediate in methanogenesis, since methanopterin or FAF is an essential component of the carbon dioxide reducing factor in dialyzed extract methanogenesis. FAF also carries the carbon at the methylene and methyl oxidation levels.(ABSTRACT TRUNCATED AT 400 WORDS)

Derivatives of methanopterin, a coenzyme involved in methanogenesis

Degradational studies of methanopterin, a coenzyme involved in methanogenesis, are reported. The results of these studies are in full accordance with the proposed structure of methanopterin as N-[1'-(2''-amino-4''-hydroxy-7'' -methyl-6''-pteridinyl)ethyl]-4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl(5'-1'' )O-alpha-ribofuranosyl-5''-phosphoric acid] aniline in which the phosphate group is esterified with alpha-hydroxyglutaric acid. Acid hydrolysis of methanopterin cleaved the 5'----1'' glycosidic bond and yielded a 'hydrolytic product' which was identified as N-[1'-(2''-amino-4''-hydroxy-7'' -methyl-6''-pteridinyl)ethyl]-4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl]aniline. Alkaline permanganate oxidation of methanopterin yielded 7-methylpterin-6-carboxylic acid. Catalytic (or enzymatic) hydrogenation of methanopterin gave a mixture of 6-ethyl-7-methyl-7,8-dihydropterin, 6-ethyl-7-methylpterin and a third compound, named methaniline which was identified as 4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl(5'----1'')O-alpha -ribofuranosyl-5''-phosphoric acid]aniline, in which the phosphate group is esterified with alpha-hydroxyglutaric acid. Methanosarcina barkeri contains a closely related coenzyme called sarcinapterin, which was identified as a L-glutamyl derivative of methanopterin, where the glutamate moiety is attached to the alpha-carboxylic acid group of the alpha-hydroxyglutaric acid moiety of methanopterin via an amide linkage.

Identification of 6-acetyl-7-methyl-7,8-dihydropterin as a degradation product of 5,10-methenyl-5,6,7,8-tetrahydromethanopterin

During purification procedures and upon aerobic heating with alkali a green-yellow degradation fluorescent product (GY) was formed from 5,10-methenyl-5,6,7,8-tetrahydromethanopterin, an intermediate in the reduction of CO2 to methane [J. T. Keltjens, L. Daniels, H. G. Janssen, and G. D. Vogels (1983) Eur. J. Biochem. 130, 545-552]. GY was suggested to be a 6-(1-oxo)-7,8-dihydropterin. On the basis of the spectral properties and the results of degradation studies, it was now shown that the structure of GY is 6-acetyl-7-methyl-7,8-dihydropterin. This structure was confirmed by synthesis of the compound and other reference substances.

Elucidation of the structure of methanopterin, a coenzyme from Methanobacterium thermoautotrophicum, using two-dimensional nuclear-magnetic-resonance techniques

Methanopterin is a coenzyme involved in methanogenesis. From 2 kg wet cells of Methanobacterium thermoautotrophicum about 35 mumol methanopterin were isolated. The structure of this compound was elucidated by various two-dimensional nuclear-magnetic-resonance techniques. Methanopterin was identified as N-[1'-(2"-amino-4"-hydroxy-7" - methyl-6"- pteridinyl) ethyl]-4-[2',3',4',5'- tetrahydroxypent-1'- yl (5' leads to 1") O-alpha-ribofuranosyl-5"-phosphoric acid] aniline, in which the phosphate group is esterified with alpha-hydroxyglutaric acid. The molecular formula of the sodium salt of methanopterin at pH 7.0 is C30H38O16N6PNa3 X chiH2O (chi is about 4). The anhydrous sodium salt of methanopterin has a molecular mass of 838.60 Da and the molar absorption coefficient at 342 nm is 7.4 mM-1 cm-1 at pH 7.0.