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Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium Formicicum NEIL L

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Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium Formicicum NEIL L JOURNAL OF BACTERIOLOGY, Feb. 1986, p. 405-411 Vol. 165, No. 2 0021-9193/86/020405-07$02.00/0 Copyright (C 1986, American Society for Microbiology Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium formicicum NEIL L. SCHAUERt AND JAMES G. FERRY* Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 Received 16 August 1985/Accepted 19 November 1985 The coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum was purified to electrophoretic homogeneity by anoxic procedures which included the addition o(f azide, flavin adenine dinucleotide (FAD), glycerol, and 2-mercaptoethanol to all buffer solutions to stabilize iictivity. The enzyme contains, in approximate miolar ratios, 1 FAD molecule and 1 molybdenum, 2 zinc, 21 to 24 iron, and 25 to 29 Downloaded from 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 olol. The molecular weight of the a-subunit is 85,000, and that of the ,-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. The methanogenic bacteria are phylogenetically distant Cells were harvested in the late log phase at an optical density from eubacteria and eucaryotes (10). Consistent with this of 3.0 to 4.5 (550 nm, 1-cm light path). Anoxic harvesting was http://jb.asm.org/ division, they utilize several unusual cofactors, including the performed by maintaining the cultures under an atmosphere low-potential electron carrier coenzyme F420 (8-hydroxy-5- of H2-CO2 (4:1) and using a model LE continuous-flow deazaflavin) (6). Several oxidation and reduction reactions centrifuge (Carl Padberg, Lehr-Baden, West Germany) are linked to coenzyme F420, including the oxidation of operated at 24,000 rpm. The cell paste was immediately formate catalyzed by formate dehydrogenase, which sup- frozen and then stored in liquid N2- plies electrons for the reduction of carbon dioxide to meth- Purification of formate dehydrogenase. Strictly anoxic ma- ane (8, 16, 27, 30). nipulations and anoxic buffer solutions were used to exclude Spectroscopic studies of the formate dehydrogenase from 02 in every step of the purification as described previously Methanobacterium formicicum indicate the presence of mo- (27). All steps were performed at 4° C. The anoxic buffer, 50 on October 25, 2018 by guest lybdenum and iron-sulfur centers (1). Present methods for mM potassium phosphate (pH 7.5), also contained 5% the purification of this enzyme result in a decrease in the rate (wt/vol) glycerol, 10 mM sodium azide, 10 F.M FAD, and 2 of coenzyme F420 reduction relative to methyl viologen mM 2-mercaptoethanol. The cell suspension (130 g of reduction (27, 28), but preincubation with flavin adenine thawed cell paste in 260 ml of buffer) was passed through a dihucleotide (FAD) restores coenzyme F420-dependent ac- French pressure cell (SLM-Aminco, Urbana, Ill.) at 1,405 tivity, sUggesting that FAD is an essential component (28). kg/cm2 and then centrifuged at 100,000 x g for 30 min. To the Studies have also identified a fluorescent pterin compound supernatant solution was added solid ammonium sulfate to associated with the enzyme (27; H. D. May, N. L. Schauer, 60% saturation (4° C) under strictly anoxic conditions as and J. G. Ferry, submitted for publication). The quantitation described previously (27). The solution was adjusted to pH of components in coenzyme F420-dependent enzymes is 7.5 by the addition of 10% (wt/vol) ammonium hydroxide. necessary to further understand their function in Precipitated protein was removed by centrifugation at intramolecular electron transfer. Here we report on the 100,000 x g for 30 min. The supernatant solutiont that composition and physical properties of the formate dehydro- contained the enzyme was applied to a DEAE-cellulose genase from M. formicicum purified to electrophoretic ho- (Whatman DE-53) column (5 by 15 cm) equilibrated with mogeneity by methods that preserve coenzyme F420- buffer 60% saturated with ammonium sulfate (25° C). The dependent activity. column was developed at pH 7.5 with a 1.2-liter linear gradient of ammonium sulfate decreasing from 40 to 20% MATERIALS AND METHODS saturation. Formate dehydrogenase-containing fractions Cell material. M. formicicum JF1 (DSM 2639) was grown with the greatest specific activity were selected, concen- in 12-liter batches as described previously (26), except that trated by ultrafiltration through a YM-30 membrane the basal medium contained the following constituents (grams (30,000-Mr cutoff; Amicon Corp., Lexington, Mass.), and per liter): NaHCO2, 6.0; NH4Cl, 1.48; K2HPO4, 1.36; loaded onto a phenyl-Sepharose CL-4B (Pharmacia, Inc., KH2PO4, 0.90; NaCl, 0.45; MgSO4, 0.045; CaCl2 * 2H20, Piscataway, N.J.) column (2.5 by 20 cm) equilibrated with 0.06; NaCH3CO2, 2.0; Na2CO3, 3.0; Na2MoO4, 0.024; buffer 20% saturated with ammonium sulfate (6° C). The cysteine hydrochloride, 0.27; Na2SeO3, 0.0002; column was developed at pH 7.5 with a linear gradient of Na2S - 9H20, 0.27; Fe(NH4)(SO4)2, 0.06; and resazurin, ammonium sulfate decreasing from 15 to 0% saturation. 0.001. Cultures were sparged with H2-CO2 (4:1) at 300 ml/min. Formate dehydrogenase-containing fractions were combined and loaded directly onto a hydroxylapatite column (2.5 by 20 * Corresponding author. cm) (Calbiochem-Behring, La Jolla, Calif.). The column was t Present address: Department of Microbiology, University of developed at pH 7.5 with a linear gradient of potassium Georgia, Athens, GA 30602. phosphate increasing from 0.05 to 0.3 M. Formate dehydro- 405 406 SCHAUER AND FERRY J. BACTERIOL. genase-containing fractions were combined and concen- Hugli and Moore (13), and the amount was calculated from trated to 5 ml by ultrafiltration as described above. the trytophan-histidine ratio. Unbound, exogenously added FAD was routinely re- (v) Metal and inorganic sulfur determinations. Iron and moved from the purified enzyme by anoxic pressure dialysis zinc were determined by atomic absorption spectroscopy on under 02-free N2 in an Amicon ultrafiltration apparatus an Instrumentation Laboratories model 351 spectrometer. equipped with a YM-30 membrane. To the enzyme solution Atomization was accomplished with an air-acetylene flame. (5 ml) was added 5 ml of FAD-free anoxic buffer, followed Samples were diluted into the working range with 2 M nitric by anoxic concentration to 5 ml. The enzyme was filtered in acid. Molybdenum was also determined by atomic absorp- this mnanner 10 times. Native FAD-depleted formate dehy- tion spectroscopy, except that the spectrometer was fitted drogenase was prepared by removing the remaining bound with an Instrumentation Laboratories model 555 graphite FAD by the same pressure dialysis procedure, except that furnace. Samples were dried under a stream of N2 (75° C), 0.5 mM formate or 1 mM sodium dithionite was added to the digested for 1 h in 1 M nitric acid (75° C), and then dried again FAD-free buffer. under N2. Samples were diluted into the working range with Analytical methods. (i) Formate dehydrogenase assay. 10 mM nitric acid. Subsamples were injected directly into Formate dehydrogenase was assayed as described previ- the graphite furnace and dried at 75° C for 25 s and at 100° C ously (27) by monitoring the formate-dependent reduction of for 25 s. Pyrolysis was done at 750° C for 30 s and at 950TC for Downloaded from coenzyme F420 at 420 nm or of methyl viologen at 603 nm. 30 s. Atomnization was done at 2,800° C for 5 s. Formate One unit of activity was the amount of enzyme that reduced dehydrogenase samples and standards for neutron activation 1 pLmol of electron acceptor per min, and the specific activity analysis were placed in polyethylene bags and irradiated for was expressed as units per milligram of protein. Coenzyme 4 h at a flux of 5 x 1013 neutrons cm-2 s-1, followed by a 1800 F420 was purified from M. formicicum as described previ- rotation and irradiation for 2 h at the same flux. Samples and ously (28). standards were counted at a distance of 20 cm after 6 days (ii) Protein determinations. Protein was determined by the and at 1 cm after approximately 6 weeks with a high- method of Bradford (3) with homogeneous formate dehydro- resolution germanium detector (GAMMA-X-1) (11). The genase as the protein standard. The standard was prepared uncertainty in concentration was one standard deviation, http://jb.asm.org/ by first concentrating the enzyme solution fivefold under based on counting statistics. 02-free N2 (60 lb/in2) and then adding anoxic distilled water Inorganic sulfide was determined by the method of Beinert to the original volume. The enzyme was filtered in this (2) in 0.5-ml culture tubes fitted with serum stoppers (7 by 15 manner six times, and the retentate was dried under vacuum mm). to a constant weight. The residue was weighed with a Cahn (vi) Analysis for bound flavin. Bound flavin was released by model 7500 electrobalance and dissolved in 50 mM potas- boiling (15 min) formate dehydrogenase solutions previotusly sium phosphate (pH 7.5). freed of exogenously added FAD. The boiled samples were (iii) Electrophoresis. Native polyacrylamide slab gel elec- centrifuged to remove precipitated protein, and the superna- trophoresis was performed with the Tris-asparagine (Sigma tant solutions were then analyzed by reconstitution of apo- on October 25, 2018 by guest Chemical Co., St.
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