Biomedical subjects

J G Ferry

Publications and source records attributed to J G Ferry.

At least 73 records · Page 4Linked to original sources

PubMed1990

Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila.

The cell extract protein content of acetate- and methanol-grown Methanosarcina thermophila TM-1 was examined by two-dimensional polyacrylamide gel electrophoresis. More than 100 mutually exclusive spots were present in acetate- and methanol-grown cells. Spots corresponding to acetate kinase, phosphotransacetylase, and the five subunits of the carbon monoxide dehydrogenase complex were identified in acetate-grown cells. Activities of formylmethanofuran dehydrogenase, formylmethanofuran:tetrahydromethanopterin formyltransferase, 5,10-methenyltetrahydromethanopterin cyclohydrolase, methylene tetrahydromethanopterin:coenzyme F420 oxidoreductase, formate dehydrogenase, and carbonic anhydrase were examined in acetate- and methanol-grown Methanosarcina thermophila. Levels of formyltransferase in either acetate- or methanol-grown Methanosarcina thermophila were approximately half the levels detected in H2-CO2-grown Methanobacterium thermoautotrophicum. All other enzyme activities were significantly lower in acetate- and methanol-grown Methanosarcina thermophila.

Acetates↗

PubMed1989

Activation of acetate by Methanosarcina thermophila. Purification and characterization of phosphotransacetylase.

Phosphotransacetylase (EC 2.3.1.8) was purified 83-fold to a specific activity of 2.5 mmol of acetyl-CoA synthesized per min/mg of protein from Methanosarcina thermophila cultivated on acetate. This rate was 10-fold greater than the rate of acetyl phosphate synthesis. The native enzyme (Mr 42,000-52,000) was a monomer and was not integral to the membrane. Activity was optimum at pH 7.0, and 35-45 degrees C. The enzyme was stable to air and to temperatures up to 70 degrees C, but was inactivated at higher temperatures. Phosphate and sulfate partially protected against heat inactivation. Potassium or ammonium ion concentrations above 10 mM were required for maximum activity of the purified enzyme; the intracellular potassium concentration of M. thermophila approximated 175 mM. Sodium, phosphate, sulfate, and arsenate ions were inhibitory to enzyme activity. Western blots of cell extracts showed that phosphotransacetylase was synthesized in higher quantity in acetate-grown cells than in methanol-grown cells.

Acetates↗

PubMed1989

Purification and properties of phloroglucinol reductase from Eubacterium oxidoreducens G-41.

Phloroglucinol reductase was purified 90-fold to homogeneity from the anaerobic rumen organism Eubacterium oxidoreducens strain G-41. The enzyme is stable in the presence of air and is found in the soluble fraction after ultracentrifugation of cell extract. Ion-exchange, hydrophobic interaction, and affinity chromatography were used to purify the enzyme. The native Mr is 78,000, and the subunit Mr is 33,000 indicating an alpha 2 homodimer. The enzyme is specific for phloroglucinol and NADPH. The Km and Vmax are 600 microM and 640 mumol min-1 mg-1 (pH 7.2) for phloroglucinol, and 6.7 microM and 550 mumol min-1 mg-1 (pH 6.8) for NADPH; the Km and Vmax for the reverse direction are 290 microM and 140 mumol min-1 mg-1 (pH 7.2) for dihydrophloroglucinol, and 27 microM and 220 mumol min-1 mg-1 (pH 7.2) for NADP. Temperature and pH optima are 40 degrees C and 7.8 in the forward direction. The pure enzyme is colorless in solution and flavins are absent. Analysis for cobalt, manganese, molybdenum, vanadium, tungsten, selenium, copper, nickel, iron, and zinc indicated that these metals are not components of the phloroglucinol reductase. Cupric chloride, n-ethylmaleimide, and p-chloromercuribenzoate are potent inhibitors of enzyme activity. The properties of phloroglucinol reductase indicate that it functions in the pathway of anaerobic degradation of trihydroxybenzenes by catalyzing reduction of the aromatic nucleus prior to ring fission.

Amino Acid Sequence↗

PubMed1989

Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum.

The membrane-associated coenzyme F420-reducing hydrogenase of Methanobacterium formicicum was purified 87-fold to electrophoretic homogeneity. The enzyme contained alpha, beta, and gamma subunits (molecular weights of 43,000, 36,700, and 28,800, respectively) and formed aggregates (molecular weight, 1,020,000) of a coenzyme F420-active alpha 1 beta 1 gamma 1 trimer (molecular weight, 109,000). The hydrogenase contained 1 mol of flavin adenine dinucleotide (FAD), 1 mol of nickel, 12 to 14 mol of iron, and 11 mol of acid-labile sulfide per mol of the 109,000-molecular-weight species, but no selenium. The isoelectric point was 5.6. The amino acid sequence I-N3-P-N2-R-N1-EGH-N6-V (where N is any amino acid) was conserved in the N-termini of the alpha subunits of the F420-hydrogenases from M. formicicum and Methanobacterium thermoautotrophicum and of the largest subunits of nickel-containing hydrogenases from Desulfovibrio baculatus, Desulfovibrio gigas, and Rhodobacter capsulatus. The purified F420-hydrogenase required reductive reactivation before assay. FAD dissociated from the enzyme during reactivation unless potassium salts were present, yielding deflavoenzyme that was unable to reduce coenzyme F420. Maximal coenzyme F420-reducing activity was obtained at 55 degrees C and pH 7.0 to 7.5, and with 0.2 to 0.8 M KCl in the reaction mixture. The enzyme catalyzed H2 production at a rate threefold lower than that for H2 uptake and reduced coenzyme F420, methyl viologen, flavins, and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Specific antiserum inhibited the coenzyme F420-dependent but not the methyl viologen-dependent activity of the purified enzyme.

Amino Acid Sequence↗

PubMed1989

Reconstitution and properties of a coenzyme F420-mediated formate hydrogenlyase system in Methanobacterium formicicum.

Formate hydrogenlyase activity in a cell extract of Methanobacterium formicicum was abolished by removal of coenzyme F420; addition of purified coenzyme F420 restored activity. Formate hydrogenlyase activity was reconstituted with three purified components from M. formicicum: coenzyme F420-reducing hydrogenase, coenzyme F420-reducing formate dehydrogenase, and coenzyme F420. The reconstituted system required added flavin adenine dinucleotide (FAD) for maximal activity. Without FAD, the formate dehydrogenase and hydrogenase rapidly lost coenzyme F420-dependent activity relative to methyl viologen-dependent activity. Immunoadsorption of formate dehydrogenase or coenzyme F420-reducing hydrogenase from the cell extract greatly reduced formate hydrogenlyase activity; addition of the purified enzymes restored activity. The formate hydrogenlyase activity was reversible, since both the cell extract and the reconstituted system produced formate from H2 plus CO2 and HCO3-.

Aldehyde Oxidoreductases↗

PubMed1988

Purification and characterization of acetate kinase from acetate-grown Methanosarcina thermophila. Evidence for regulation of synthesis.

Acetate kinase was purified 102-fold to a specific activity of 656 mumol of ADP formed/min/mg of protein from acetate-grown Methanosarcina thermophila. The enzyme was not intrinsically membrane bound. The native enzyme (Mr 94,000) was an alpha 2 homodimer with a subunit Mr of 53,000. The activity was optimum between pH 7.0 and 7.4. A pI of 4.7 was determined. The enzyme was stable to O2 and stable to heating at 70 degrees C for 15 min but was rapidly inactivated at higher temperatures. The apparent Km for acetate was 22 mM and for ATP was 2.8 mM. The enzyme phosphorylated propionate at 60% of the rate with acetate but was unable to use formate. TTP, ITP, UTP, GTP, and CTP replaced ATP as the phosphoryl donor to acetate. The enzyme required one of several divalent cations for activity; the maximum rate was obtained with Mn2+. Western blots of cell extract proteins showed that acetate grown cells synthesized higher quantities of the acetate kinase than did methanol grown cells.

Acetate Kinase↗

PubMed1988

Ferredoxin requirement for electron transport from the carbon monoxide dehydrogenase complex to a membrane-bound hydrogenase in acetate-grown Methanosarcina thermophila.

Cell extracts from acetate-grown Methanosarcina thermophila contained CO-oxidizing:H2-evolving activity 16-fold greater than extracts from methanol-grown cells. Following fractionation of cell extracts into soluble and membrane components, CO-dependent H2 evolution and CO-dependent methyl-coenzyme M methylreductase activities were only present in the soluble fraction, but addition of the membrane fraction enhanced both activities. A b-type cytochrome(s), present in the membrane fraction, was linked to a membrane-bound hydrogenase. CO-oxidizing:H2-evolving activity was reconstituted with: (i) CO dehydrogenase complex, (ii) a ferredoxin, and (iii) purified membranes with associated hydrogenase. The ferredoxin was a direct electron acceptor for the CO dehydrogenase complex. The ferredoxin also coupled CO oxidation by CO dehydrogenase complex to metronidazole reduction.

Acetates↗

PubMed1988

Purification and characterization of a ferredoxin from acetate-grown Methanosarcina thermophila.

A ferredoxin, which functions as an electron acceptor for the CO dehydrogenase complex from Methanosarcina thermophila, was purified from acetate-grown cells. It was isolated as a trimer having a native molecular weight of approximately 16,400 and monomer molecular weight of 4,888 calculated from the amino acid composition. The ferredoxin contained 2.80 +/- 0.56 Fe atoms and 1.98 +/- 0.12 acid-labile sulfide. UV-visible absorption maxima were 395 and 295 nm with monomeric extinction coefficients of epsilon 395 = 12,800 M-1 cm-1 and epsilon 295 = 14,460 M-1 cm-1. The A395/A295 ratio ranged from 0.80 to 0.88. There were 5 cysteines per monomer but no methionine, histidine, arginine, or aromatic amino acids. The N-terminal amino acid sequence showed a 4-cysteine cluster with potential to coordinate a Fe:S center. The protein was stable for 30 min at 70 degrees C, but denatured during incubation at 85 degrees C.

Acetates↗

PubMed1988

Isolation and characterization of "Methanosphaera cuniculi" sp. nov.

A nonmotile, gram-positive, spherical organism was isolated from the intestinal tracts of rabbits. Both hydrogen and methanol were required for growth. No methane was produced from hydrogen-carbon dioxide, formate, acetate, methylamines, ethanol, or isopropanol. The optimum pH was 6.8, and the optimum temperature was 35 to 40 degrees C. The DNA G+C content is 23 mol%. The pseudomurein cell wall contained serine. These characteristics and the immunological fingerprinting results are consistent with its placement in the genus Methanosphaera as a new species.

Animals↗

PubMed1988

Effect of molybdenum and tungsten on synthesis and composition of formate dehydrogenase in Methanobacterium formicicum.

The influence of sodium molybdate and sodium tungstate on formate dehydrogenase activity was studied in H2-CO2-grown cultures of Methanobacterium formicicum. Depletion of molybdate from the growth medium resulted in a 75-fold decrease of intracellular molybdenum and a 35-fold decrease in enzyme activity; however, growth rate and cell yields were not influenced. By using an indirect enzyme-linked immunoassay, the amount of formate dehydrogenase approximated 3% of the total protein in cells grown in the presence of molybdate. Molybdenum-starved cells contained approximately 15-fold less formate dehydrogenase protein; Western blot (immunoblot) analysis revealed that both subunits of the enzyme were synthesized. Molybdenum starvation resulted in an increase in the amount of mRNA that hybridized to fdh-specific DNA. The results indicated an inverse relationship between the amount of transcript and the amount of formate dehydrogenase protein detected in response to molybdenum starvation. The addition of 1 mM tungstate to molybdate-containing media resulted in nearly complete loss of enzyme activity and decreased the intracellular concentration of molybdenum 10-fold. Cells grown in the presence of tungstate synthesized high amounts of inactive formate dehydrogenase and contained mRNA that hybridized to fdh-specific DNA in amounts similar to that in cells grown with sufficient molybdate. Inactive formate dehydrogenase, purified from cells grown in the presence of tungstate, had the same subunit composition and contained amounts of molybdopterin cofactor, albeit metal-free, comparable to those in the active enzyme.

Aldehyde Oxidoreductases↗

PubMed1988

Characterization of the upstream region of the formate dehydrogenase operon of Methanobacterium formicicum.

The fdhA and fdhB genes of Methanobacterium formicicum, which code for the alpha and beta subunits of formate dehydrogenase, were cotranscribed as part of a large transcript. By using Northern (RNA) gel blot analysis, the transcription start site was located within a 1.6-kilobase BglII-NcoI fragment 4.3 kilobases upstream from the fdhA gene. The precise transcription start site within the fragment was determined with the aid of primer extension analysis and S1 nuclease protection studies. A putative promoter sequence for structural genes of methanogenic archaebacteria is proposed based on a comparison of DNA sequences of the upstream region of methanogen operons for which transcription initiation sites are known. Comparison of the DNA sequence of the upstream region of the fdh operon of M. formicicum with the sequence upstream of the fdhF gene of Escherichia coli revealed regions of considerable identity.

Aldehyde Oxidoreductases↗

PubMed1988

Digesta flows in sheep fed poor-quality hay supplemented with urea and carbohydrates.

Two metabolism trials were conducted with 12 yearling crossbred wethers per trial (34 and 38 kg for trials 1 and 2, respectively). The wethers, equipped with ruminal, abomasal and ileal cannulae, were randomly allotted for each trial to the following treatments: 1) hay alone or hay supplemented with 2) .9% urea, 3) 1% urea and 6.5% molasses or 4) 1% urea and 5.2% corn. Two digestive flow markers were used: Cr2O3 powder and Co-ethylenediaminetetraacetic acid (Co-EDTA). Urea and Co-EDTA were infused continuously into the rumen via cannula. Daily dry matter (DM) intake averaged 517 g. Urea supplementation improved N retention (P less than .01). Apparent digestibility of DM, acid detergent fiber (ADF) and energy was not affected by treatment. Urea and carbohydrate supplementation increased ruminal propionic acid molar proportions (P less than .05). Apparent ruminal DM digestion accounted for 41% of the total DM degraded, whereas 77.4% of the digestible ADF was degraded in the rumen. Urea supplementation increased ADF digestion in the large intestine (P less than .01). Urea and carbohydrate supplementation resulted in a stepwise increase in N flowing with the liquid phase at the abomasum. Mean retention times of the solid and liquid phases of digestive contents were similar across treatments. Overall, benefits of supplementation of poor-quality fescue hay diets by small amounts of urea and readily available carbohydrates remain questionable for sheep fed at a fixed level of intake below maintenance.

Animal Feed↗

PubMed1987

EPR properties of the Ni-Fe-C center in an enzyme complex with carbon monoxide dehydrogenase activity from acetate-grown Methanosarcina thermophila. Evidence that acetyl-CoA is a physiological substrate.

The carbon monoxide dehydrogenase complex from acetate-grown Methanosarcina thermophila was further studied by EPR spectroscopy. The as purified enzyme exhibited no paramagnetic species at 113 K; however, enzyme reduced with CO exhibited a complex EPR spectrum comprised of two paramagnetic species with g values of g1 = 2.089, g2 = 2.078, and g3 = 2.030 (signal I) and g1 = 2.057, g2 = 2.049, and g3 = 2.027 (signal II). Isotopic substitution with 61Ni, 57Fe, or 13CO resulted in broadening of the EPR spectra indicating a Ni-Fe-C spin-coupled complex. Pure signal II was obtained following treatment of the CO-reduced enzyme with acetyl-CoA but not by addition of acetyl phosphate or CoASH. Acetate-grown cells were highly enriched in acetate kinase (EC 2.7.2.1) and CoASH-dependent phosphotransacetylase (EC 2.3.1.8) activities. These results suggest acetyl-CoA is a physiological substrate for the carbon monoxide dehydrogenase complex synthesized in acetate-grown cells of M. thermophila.

Acetate Kinase↗

PubMed1987

Locations of the hydrogenases of Methanobacterium formicicum after subcellular fractionation of cell extract.

The F420 hydrogenase of Methanobacterium formicicum was associated with membranes isolated by sucrose density gradient ultracentrifugation of cell extract. The methyl viologen hydrogenase was present in the soluble fractions. Column chromatography with phenyl-Sepharose CL-4B revealed that the F420 hydrogenase was strongly hydrophobic, suggesting that it associates with isolated membranes through hydrophobic interactions.

Cell Fractionation↗

PubMed1986

Mechanistic studies of the coenzyme F420 reducing formate dehydrogenase from Methanobacterium formicicum.

Mechanistic studies have been undertaken on the coenzyme F420 dependent formate dehydrogenase from Methanobacterium formicicum. The enzyme was specific for the si face hydride transfer to C5 of F420 and joins three other F420-recognizing methanogen enzymes in this stereospecificity, consistent perhaps with a common type of binding site for this 8-hydroxy-5-deazariboflavin. While catalysis probably occurs by hydride transfer from formate to the enzyme to generate an EH2 species and then by hydride transfer back out to F420, the formate-derived hydrogen exchanged with solvent protons before transfer back out to F420. The kinetics of hydride transfer from formate revealed that this step is not rate determining, which suggests that the rate-determining step is an internal electron transfer. The deflavo formate dehydrogenase was amenable to reconstitution with flavin analogues. The enzyme was sensitive to alterations in FAD structure in the 6-, 7-, and 8-loci of the benzenoid moiety in the isoalloxazine ring.

Aldehyde Oxidoreductases↗

PubMed1986

Cloning, expression, and nucleotide sequence of the formate dehydrogenase genes from Methanobacterium formicicum.

The genes for the two subunits of the formate dehydrogenase from Methanobacterium formicicum were cloned and their sequences determined. When expressed in Escherichia coli, two proteins were produced which had the appropriate mobility on an SDS gel for the two subunits of formate dehydrogenase and cross-reacted with antibodies raised to purified formate dehydrogenase. The genes for the two formate dehydrogenase subunits overlap by 1 base pair and are preceded by DNA sequences similar to both eubacterial and archaebacterial promoters and ribosome-binding sites. The amino acid sequences deduced from the DNA sequence were analyzed, and the arrangement of putative iron-sulfur centers is discussed.

Aldehyde Oxidoreductases↗

PubMed1986

Composition of the coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum.

The coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum was purified to electrophoretic homogeneity by anoxic procedures which included the addition of azide, flavin adenine dinucleotide (FAD), glycerol, and 2-mercaptoethanol to all buffer solutions to stabilize activity. The enzyme contains, in approximate molar ratios, 1 FAD molecule and 1 molybdenum, 2 zinc, 21 to 24 iron, and 25 to 29 inorganic sulfur atoms. Denaturation of the enzyme released a molybdopterin cofactor. The enzyme has a molecular weight of 177,000 and consists of one each of two different subunits, giving the composition alpha 1 beta 1. The molecular weight of the alpha-subunit is 85,000, and that of the beta-subunit is 53,000. The UV-visible spectrum is typical of nonheme iron-sulfur flavoprotein. Reduction of the enzyme facilitated dissociation of FAD, and the FAD-depleted enzyme was unable to reduce coenzyme F420. Preincubation of the FAD-depleted enzyme with FAD restored coenzyme F420-dependent activity.

Aldehyde Oxidoreductases↗

PubMed1986

Molybdopterin cofactor from Methanobacterium formicicum formate dehydrogenase.

The molybdopterin cofactor from the formate dehydrogenase of Methanobacterium formicicum was studied. The cofactor was released by guanidine denaturation of homogeneous enzyme, which also released greater than 80% of the molybdenum present in the enzyme. The anoxically isolated cofactor was nonfluorescent, but after exposure to air it fluoresced with spectra similar to those of described molybdopterin cofactors. Aerobic release from acid-denatured formate dehydrogenase in the presence of I2 and potassium iodide produced a mixture of fluorescent products. Alkaline permanganate oxidation of the mixture yielded pterin-6-carboxylic acid as the only detectable fluorescent product. The results showed that the cofactor from formate dehydrogenase contained a pterin nucleus with a 6-alkyl side chain of unknown structure. Covalently bound phosphate was also present. The isolated cofactor was unable to complement the cofactor-deficient nitrate reductase of the Neurospora crassa nit-1 mutant.

Aldehyde Oxidoreductases↗