Studies of sulfate utilization by algae: 8. The ubiquity of sulfate reduction to thiosulfate

Cell-free extracts from several microorganisms, when prepared by methods originally devised for Chlorella pyrenoidosa (Emerson strain 3) and incubated anaerobically with ATP, Mg²⁺, and 2, 3-dimercaptopropan-1-ol, are capable of reducing sulfate-³⁵S to thiosulfate. These microorganisms include, in addition to C. pyrenoidosa (Emerson strain 3), several other strains of C. pyrenoidosa, Chlorella protothecoides, Chlorella vulgaris, Anacystis sp., Chlamydomonas reinhardi, Escherichia coli, Salmonella typhimurium, and baker's yeast. Three of these organisms, E. coli, S. typhimurium, and baker's yeast, were previously reported by others to reduce sulfate to sulfite. Moreover, three mutant strains of S. typhimurium (Ba-25, Ce-363, and Bc-482) previously reported by other workers to be unable to reduce sulfate to sulfite also cannot form thiosulfate, and one mutant strain (Cd-68) reportedly able to form sulfite can also form thiosulfate. Taken together, this suggests that thiosulfate-forming activity may be a common feature of sulfate-reducing systems, and it may be present in enzymatic systems previously thought to be forming sulfite. Reasonably conclusive identification of thiosulfate is provided by ion exchange chromatography and by paper electrophoresis; the ambiguities associated with other analytical methods are discussed.     

Studies of sulfate utilization by algae. 5. Identification of thiosulfate as a major Acid-volatile product formed by a cell-free sulfate-reducing system from chlorella

Separation of the products formed from sulfate-³⁵S by cell-free extracts of Chlorella pyrenoidosa (Emerson Strain 3) has permitted the identification of thiosulfate as a major product which yields acid-volatile radioactivity. The products formed, as separated by Dowex-1-nitrate chromatography, are qualitatively the same whether extracts at pH 7.0 (using TPNH as the reductant) or extracts at pH 9 [using 2,3-dimercaptopropan-1-ol, (BAL) as reductant] are employed. While thiosulfate can be separated without the addition of carrier, the inclusion of carrier improves the recovery. High concentrations of ATP which have been shown previously to inhibit the formation of acid-volatile radioactivity from radioactive sulfate, inhibit the formation of thiosulfate almost completely. Degradation of the thiosulfate formed at normal ATP concentrations reveals that most of the radioactivity is in the SO₃-sulfur of the molecule suggesting that the SH-sulfur is derived from the enzyme extracts. If carrier sulfite is present during thiosulfate formation from sulfate-³⁵S, radioactive sulfite is recovered at the expense of radioactive thiosulfate. Reconstruction experiments utilizing specifically-labeled thiosulfates indicate that radioactive sulfite formation is probably not the result of trapping a normal intermediate, but can be attributed to non-enzymatic exchange between labeled thiosulfate formed from sulfate and the non-radioactive sulfite added, suggesting that free sulfite is not an intermediate in thiosulfate formation from sulfate.     

Characterization of a Thermolabile Sulfite Reductase from Salmonella pullorum

The biochemical basis for sulfite accumulation by sulfate-using revertants of Salmonella pullorum was determined. All of the sulfate-using mutants isolated from wild-type S. pullorum accumulated sulfite when grown at 37 but not at 25 C. The specific activity of reduced nicotinamide adenine dinucleotide (NADPH)-dependent sulfite reductase (H ₂S-NADP oxidoreductase, EC 1.8.1.2) and of reduced methyl viologen (MVH)-dependent sulfite reductase (H ₂S-MV oxidoreductase), in extracts prepared from cells incubated at 37 C, declined as the incubation period lengthened. However, the specific activity of both reductases from cells incubated at 25 C did not decline. Thermolability of cell-free NADPH-dependent sulfite reductase from cells of S. pullorum incubated at 37 C was greater than the lability of this enzyme either from cells of S. typhimurium incubated at 37 C or from cells of S. pullorum incubated at 25 C. Cells cultured at 37 C continued to accumulate sulfite when the incubation temperature was shifted to 25 C; cells cultured at 25 C and shifted to 37 C accumulated no sulfite, whereas these cells shifted to 41 C accumulated sulfite. It was concluded that the configuration of the sulfite reductase of S. pullorum strain 6–18 is a function of the incubation temperature at which synthesis occurs.     

Nucleoplasmin-mediated chromatin remodelling is required for Xenopus sperm nuclei to become licensed for DNA replication

During late mitosis and early G₁, a series of proteins are assembled onto replication origins, resulting in them becoming ‘licensed’ for replication in the subsequent S phase. Four factors have so far been identified that are required for chromatin to become functionally licensed: ORC (the origin recognition complex) and Cdc6, plus the two components of the replication licensing system RLF-M and RLF-B. Here we describe the first steps of a systematic fractionation of Xenopus egg extracts to identify all the components necessary for the assembly of licensed replication origins on Xenopus sperm nuclei (the physiological DNA substrate in this system). We have purified a new activity essential for this reaction, and have shown that it is nucleoplasmin, a previously known chromatin remodelling protein. Nucleoplasmin decondenses the sperm chromatin by removing protamines, and is required at the earliest known step in origin assembly to allow ORC to bind to the DNA. Sperm nuclei can be licensed by a combination of nucleoplasmin, RLF-M and a partially purified fraction that contains ORC, Cdc6 and RLF-B. This suggests that we are likely to have identified most of the proteins required for this assembly reaction.     

The procaryotic nature of the fatty acid synthetase of developing Carthamus tinctorius L. (safflower) seeds

All component activities involved in the synthesis of fatty acid were detected in crude extracts of developing safflower seeds. The crude extracts were fractionated into three portions by polyethylene glycol (0–5, 5–15, and 15% supernatant). Acetyl-CoA:acyl carrier protein (ACP) transacylase was precipitated about 66% by 5% polyethylene glycol. β-Ketoacyl-ACP reductase and enoyl-ACP reductase I were completely recovered in the 5–15% fraction. β-Ketoacyl-ACP synthetase and enoyl-ACP reductase II were in the 15% supernatant fraction. Malonyl-CoA:ACP transacylase and β-hydroxyacyl-ACP dehydrase were distributed into both fractions of 5–15 and 15% supernatant. When the 5–15% fraction was gel-filtrated on Sephadex G-200 column, β-hydroxyacyl-ACP dehydrase and malonyl-CoA:ACP transacylase were clearly separated from other enzymes, but β-Ketoacyl-ACP reductase and enoyl-ACP reductase I overlapped. However, by hydroxyapatite chromatography, these two reductases were clearly separated. Properties of each enzyme were examined with the samples fractionated by polyethylene glycol. β-Ketoacyl-ACP reductase preferably utilized NADPH (K_m = 16 μM) as hydrogen donor. The K_m for acetoacetyl-ACP was 9 μm. β-Hydroxyacyl-ACP dehydrase had a K_m of 12 μm for crotonyl-ACP. Enoyl-ACP reductase had two forms, I and II, and these two reductases differed from each other as follows: (a) separation by polyethylene glycol (15%) fractionation; (b) the optimum pH; (c) the hydrogen donor specificity; (d) the substrate specificity. From these results, it is concluded that the FAS system of developing safflower seeds was nonassociated and similar to the procaryotic type of Escherichia coli.     

A Two-Component Monooxygenase Catalyzes Both the Hydroxylation of p-Nitrophenol and the Oxidative Release of Nitrite from 4-Nitrocatechol in Bacillus sphaericus JS905

Bacteria that metabolize p-nitrophenol (PNP) oxidize the substrate to 3-ketoadipic acid via either hydroquinone or 1,2,4-trihydroxybenzene (THB); however, initial steps in the pathway for PNP biodegradation via THB are unclear. The product of initial hydroxylation of PNP could be either 4-nitrocatechol or 4-nitroresorcinol. Here we describe the complete pathway for aerobic PNP degradation by Bacillus sphaericus JS905 that was isolated by selective enrichment from an agricultural soil in India. Washed cells of PNP-grown JS905 released nitrite in stoichiometric amounts from PNP and 4-nitrocatechol. Experiments with extracts obtained from PNP-grown cells revealed that the initial reaction is a hydroxylation of PNP to yield 4-nitrocatechol. 4-Nitrocatechol is subsequently oxidized to THB with the concomitant removal of the nitro group as nitrite. The enzyme that catalyzed the two sequential monooxygenations of PNP was partially purified and separated into two components by anion-exchange chromatography and size exclusion chromatography. Both components were required for NADH-dependent oxidative release of nitrite from PNP or 4-nitrocatechol. One of the components was identified as a reductase based on its ability to catalyze the NAD(P)H-dependent reduction of 2,6-dichlorophenolindophenol and nitroblue tetrazolium. Nitrite release from either PNP or 4-nitrocatechol was inhibited by the flavoprotein inhibitor methimazole. Our results indicate that the two monooxygenations of PNP to THB are catalyzed by a single two-component enzyme system comprising a flavoprotein reductase and an oxygenase.     

C(4) Photosynthesis: Light-dependent CO(2) Fixation by Mesophyll Cells, Protoplasts, and Protoplast Extracts of Digitaria sanguinalis

Mesophyll cells, protoplasts, and protoplast extracts of Digitaria sanguinalis were used for comparative studies of light-dependent CO₂ fixation. CO₂ fixation was low without the addition of organic substrates. Pyruvate, oxaloacetate, and 3-phosphoglycerate induced relatively low rates (10 to 90 μmoles/mg chlorophyll·hr) of CO₂ fixation when added separately. However, a highly synergistic relationship was found between pyruvate + oxaloacetate and pyruvate + 3-phosphoglycerate for inducing light-dependent CO₂ fixation in the mesophyll preparations. Highest rates of CO₂ fixation were obtained with protoplast extracts. Pyruvate, in combination with oxaloacetate or 3-phosphoglycerate induced light-dependent rates from 150 to 380 μmoles of CO₂ fixed/mg chlorophyll·hr which are equivalent to or exceed reported rates of whole leaf photosynthesis in C₄ species. Concentrations of various substrates required to give half-maximum velocities of CO₂ fixation were determined, with the protoplast extracts generally saturating at the lowest substrate concentrations. Chloroplasts separated from protoplast extracts showed little capacity for CO₂ fixation. The results suggest that CO₂ fixation in C₄ mesophyll cells is dependent on chloroplasts and extrachloroplastic phosphoenolpyruvate carboxylase.     

Separation of Chlorophylls c(1) and c(2) from Pigment Extracts of Pavlova gyrans by Reversed-Phase High Performance Liquid Chromatography

Chlorophylls c₁ and c₂ have been separated from total pigment extracts of the alga Pavlova gyrans Butcher using a reversed-phase high-performance liquid chromatography system. Pigments were separated on a 5 micrometer C₁₈ column (25 centimeters × 4.6 millimeters) using a gradient of methanol-acetonitrile-water. Other photosynthetic pigments were also well resolved by the system used. The separation system described may replace current thin layer chromatography methods for qualitative and quantitative determination of chlorophyll c species.     

Anaerobic Aryl Reductive Dehalogenation of Halobenzoates by Cell Extracts of “Desulfomonile tiedjei”

We studied the transformation of halogenated benzoates by cell extracts of a dehalogenating anaerobe, “Desulfomonile tiedjei.” We found that cell extracts possessed aryl reductive dehalogenation activity. The activity was heat labile and dependent on the addition of reduced methyl viologen, but not on that of reduced NAD, NADP, flavin mononucleotide, flavin adenine dinucleotide, desulfoviridin, cytochrome c₃, or benzyl viologen. Dehalogenation activity in extracts was stimulated by formate, CO, or H₂, but not by pyruvate plus coenzyme A or by dithionite. The pH and temperature optima for aryl dehalogenation were 8.2 and 35°C, respectively. The rate of dehalogenation was proportional to the amount of protein in the assay mixture. The substrate specificity of aryl dehalogenation activity for various aromatic compounds in “D. tiedjei” cell extracts was identical to that of whole cells, except differences were observed in the relative rates of halobenzoate transformation. Dehalogenation was 10-fold greater in “D. tiedjei” extracts prepared from cells cultured in the presence of 3-chlorobenzoate, suggesting that the activity was inducible. Aryl reductive dehalogenation in extracts was inhibited by sulfite, sulfide, and thiosulfate, but not sulfate. Experiments with combinations of substrates suggested that cell extracts dehalogenated 3-iodobenzoate more readily than either 3,5-dichlorobenzoate or 3-chlorobenzoate. Dehalogenation activity was found to be membrane associated. This is the first report characterizing aryl dehalogenation activity in cell extracts of an obligate anaerobe.     

The preparation of UDP-N-acetylgalactosamine from UDP-N-acetylglucosamine employing UDP-N-acetylglucosamine-4-epimerase

A rapid, simple, and inexpensive method has been developed for preparing UDP-N-acetylgalactosamine in amounts sufficient for several thousand assays of enzymes that employ this nucleotide sugar as substrate. The UDP-N-acetylglucosamine-4-epimerase in extracts of porcine submaxillary glands was used to convert UDP-N-acetylglucosamine to an equilibrium mixture of UDP-N-acetylglucosamine and UDP-N-acetylgalactosamine (molar ratio, 77:23). The two nucleotide sugars were separated from components in the extract by ion-exchange chromatography and then separated from one another by affinity chromatography on a column of Griffonia simplicifolia lectin I bound to agarose. The UDP-N-acetylgalactosamine was obtained in pure form by ion-exchange chromatography in an overall yield of 91% from the equilibrium mixture. The separation of the two nucleotide sugars by affinity chromatography also provides a rapid assay for the UDPGlcNAc-4-epimerase, which is more accurate and less time consuming than earlier published assays.     

Sulfite formation by wine yeasts

The enzyme catalyzing the reduction of sulfite by reduced benzyl viologen (BVH) was partially purified and characterized from two strains of wine yeasts, a sulfite-producing strain and a non-producing strain.Both enzymes showed corresponding features in pH-optima, optima of buffer and benzyl viologen concentrations.The enzymes did not catalyze the reduction of nitrite by reduced viologen dyes, but the reduction of sulfite was uncompetitively inhibited by nitrite. Compounds of sulfur metabolism such as sulfate, thiosulfate, cysteine, serine and methionine did not influence the activity of either of the enzymes. The main differences between the two enzymes exist in the specific activities in crude extracts, the K _m -values for sulfite, substrate inhibition rates, and localization in different fractions during (NH₄)₂SO₄ precipitation. The specific activity in crude extracts of the sulfite-producing strain (0.052 moles S^2- x min^-1 x mg^-1) was about three fold higher than that of the non-producing strain (0.0179 moles S^2- x min^-1 x mg^-1). On the other hand the sulfite-producing strain had a higher K _m -value for sulfite (2×10^-3 M) and was more strongly inhibited by the substrate than the non-producing strain (6×10^-3 M).     

Characterization of a novel thiosulfate-forming enzyme isolated from Desulfovibrio vulgaris.

An enzyme that formed thiosulfate from bisulfite and trithionate was purified from extracts of Desulfovibrio vulgaris. This enzyme, designated as "thiosulfate-forming" enzyme, required the presence of both bisulfite and trithionate. Various 35S-labeling studies showed that thiosulfate was formed from bisulfite and the inner sulfur atom of trithionate. This involved a nucleophilic attack by the bisulfite ion, resulting in the displacement of the two outer sulfonate groups of trithionate that recycled to participate as free bisulfite in subsequent reactions. This reaction required a reduction, presumably by a concerted mechanism with thiosulfate formation. The natural electron carrier cytochrome c3 participated in this reductive formation of thiosulfate. This reaction was coupled to the bisulfite reductase-catalyzed reaction, which resulted in the reconstruction of a thiosulfate-forming pathway from bisulfite.     

Properties of a NADH-dependent N-hydroxy amine reductase isolated from pig liver microsomes

A multicomponent enzyme system that catalyzes the reduction of hydroxylamine and a number of its mono- and disubstituted derivatives by NADH has been isolated from microsomes. Three protein fractions isolated from pig liver microsomes are required to reconstitute NADH-hydroxylamine reductase activity. Two of the proteins appear identical with detergent-extracted cytochrome b₅, and its flavoprotein reductase. The third protein fraction required for activity differs from previously isolated microsomal proteins. This fraction is free from detectable chromophores that absorb in the visible region of the spectrum and also appears free from metals. The properties of the NADH-hydroxylamine reductase reconstituted with the three components isolated from microsomes appears similar to the particle-bound system with respect to nucleotide and N-hydroxylamine substrate specificity.     

MET2 affects production of hydrogen sulfide during wine fermentation

The production of hydrogen sulfide (H₂S) during yeast fermentation contributes negatively to wine aroma. We have mapped naturally occurring mutations in commercial wine strains that affect production of H₂S. A dominant R₃₁₀G mutant allele of MET2, which encodes homoserine O-acetyltransferase, is present in several wine yeast strains as well as in the main lab strain S288c. Reciprocal hemizygosity and allele swap experiments demonstrated that the MET2 _R310G allele confers reduced H₂S production. Mutations were also identified in genes encoding the two subunits of sulfite reductase, MET5 and MET10, which were associated with reduced H₂S production. The most severe of these, an allele of MET10, showed five additional phenotypes: reduced growth rate on sulfate, elevated secretion of sulfite, and reduced production in wine of three volatile sulfur compounds: methionol, carbon disulfide and methylthioacetate. Alleles of MET5 and MET10, but not MET2, affected H₂S production measured by colour assays on BiGGY indicator agar, but MET2 effects were seen when bismuth was added to agar plates made with Sauvignon blanc grape juice. Collectively, the data are consistent with the hypothesis that H₂S production during wine fermentation results predominantly from enzyme activity in the sulfur assimilation pathway. Lower H₂S production results from mutations that reduce the activity of sulfite reductase, the enzyme that produces H₂S, or that increase the activity of l-homoserine-O-acetyltransferase, which produces substrate for the next step in the sulfur assimilation pathway.     

Purification and properties of the hexosaminidase A-activating protein from human liver

Human liver extracts contain an activating protein which is required for hexosaminidase A-catalysed hydrolysis of the N-acetylgalactosaminyl linkage of G_M2 ganglioside [N-acetylgalactosaminyl-(N-acetylneuraminyl) galactosylglucosylceramide]. A partially purified preparation of human liver hexosaminidase A that is substantially free of G_M2 ganglioside hydrolase activity is used to assay the activating protein. The proceudres of heat and alcohol denaturation, ion-exchange chromatography and gel filtration were used to purify the activating protein over 100-fold from crude human liver extracts. When the purified activating protein is analysed by polyacrylamide-gel disc electrophoresis, two closely migrating protein bands are seen. When purified activating protein is used to reconstitute the G_M2 ganglioside hydrolase activity, the rate of reaction is proportional to the amount of hexosaminidase A used. The activation is specific for G_M2 ganglioside and and hexosaminidase A. The activating protein did not stimulate hydrolysis of asialo-G_M2 ganglioside by either hexosaminidase A or B. Hexosaminidase B did not catalyse hydrolysis of G_M2 ganglioside with or without the activator. Kinetic experiments suggest the presence of an enzyme–activator complex. The dissociation constant of this complex is decreased when higher concentrations of substrate are used, suggesting the formation of a ternary complex between enzyme, activator and substrate. Determination of the molecular weight of the activating protein by gel-filtration and sedimentation-velocity methods gave values of 36000 and 39000 respectively.     

Resolution and Reconstitution of a Mammalian Membrane

The problem of the resolution and reconstitution of the inner mitochondrial membrane has been approached at three levels. (1) Starting with phosphorylating submitochondrial particles, a "resolution from without" can be achieved by stripping of surface components. The most extensive resolution was recently obtained with the aid of silicotungstate. Such particles require for oxidative phosphorylation the addition of several coupling factors as well as succinate dehydrogenase. (2) Starting with submitochondrial particles that have been degraded by trypsin and urea a resolution of the inner membrane proper containing an ATPase has been achieved. These experiments show that at least five components are required for the reconstitution of an oligomycin-sensitive ATPase: a particulate component, F ₁, Mg⁺⁺, phospholipids, and F_c. Morphologically, the reconstituted ATPase preparations resemble submitochondrial particles. (3) Starting with intact mitochondria individual components of the oxidation chain have been separated from each other. The following components were required for the reconstitution of succinoxidase: succinate dehydrogenase, cytochrome b\, cytochrome c ₁, cytochrome c, cytochrome oxidase, phospholipids and Q ₁₀. The reconstituted complex had properties similar to those of phosphorylating submitochondrial particles; i.e., the oxidation of succinate by molecular oxygen was highly sensitive to antimycin.     

Purification and Characterization of the Alkene Monooxygenase from Nocardia corallina B-276

Alkene monooxygenase from the propene utilizer Nocardia corallina B-276 was separated into three components, and all components were purified to homogeneity and their properties were examined. The epoxidase, with a molecular mass of 95 kDa, was considered to catalyze the oxidation of the substrate propene to propylene oxide. It consisted of 53- and 35-kDa subunits, which contained approximately 2-mol of non-heme iron per mole of protein. The reductase, molecular mass 40 kDa, was found to contain an FAD and an Fe₂ S₂ cluster. A third protein, which we have called the coupling protein, with a mass of 14 kDa, appears to function as a regulator of activity. The purified AMO system required NADH as an electron donor, and catalyzed alkene epoxidation only. Acetylene, a specific inhibitor for methane monooxygenase, did not inhibit the AMO activity.     

Plant Sources of Chinese Herbal Remedies: Laboratory Efficacy,Suppression of Meloidogyne javanica in Soil,and Phytotoxicity Assays

Extracts of Chinese herbal medicines from plants representing 13 families were tested for their ability to suppress plant-parasitic nematodes. Effective concentration (EC₅₀ and EC₉₀) levels for 18 of the extracts were determined in laboratory assays with Meloidogyne javanica juveniles and all stages of Pratylenchus vulnus. Efficacy of 17 extracts was tested against M. javanica in soil. Generally, EC₅₀ and EC₉₀ values determined in the laboratory were useful indicators for application rates in the soil. Extracts tested from plants in the Liliaceae reduced galling of tomato by M. javanica and were not phytotoxic. Similarly, isothiocyanate-yielding plants in the Brassicaceae suppressed root galling without phytotoxicity. Other plant extracts, including those from Azadirachta indica, Nerium oleander, and Hedera helix, suppressed root galling but were phytotoxic at the higher concentrations tested. Many of these plant sources have been tested elsewhere. Inconsistency in results across studies points to the need for identification of active components and for determination of concentration levels of these components when plant residues or extracts are applied to soil.     

Hydrogenase Activity and the H2-Fumarate Electron Transport System in Bacteroides fragilis

Hydrogenase activity and the H₂-fumarate electron transport system in a carbohydrate-fermenting obligate anaerobe, Bacteroides fragilis, were investigated. In both whole cells and cell extracts, hydrogenase activity was demonstrated with methylene blue, benzyl viologen, flavin mononucleotide, or flavin adenine dinucleotide as the electron acceptor. A catalytic quantity of benzyl viologen or ferredoxin from Clostridium pasteurianum was required to reduce nicotinamide adenine dinucleotide or nicotinamide adenine dinucleotide phosphate with H₂. Much of the hydrogenase activity appeared to be associated with the soluble fraction of the cell. Fumarate reduction to succinate by H₂ was demonstrable in cell extracts only in the presence of a catalytic quantity of benzyl viologen, flavin mononucleotide, flavin adenine dinucleotide, or ferredoxin from C. pasteurianum. Sulfhydryl compounds were not required for fumarate reduction by H₂, but mercaptoethanol and dithiothreitol appeared to stimulate this activity by 59 and 61%, respectively. Inhibition of fumarate reduction by acriflavin, rotenone, 2-heptyl-4-hydroxyquinoline-N-oxide, and antimycin A suggest the involvement of a flavoprotein, a quinone, and cytochrome b in the reduction of fumarate to succinate. The involvement of a quinone in fumarate reduction is also apparent from the inhibition of fumarate reduction by H₂ when cell extracts were irradiated with ultraviolet light. Based on the evidence obtained, a possible scheme for the flow of electrons from H₂ to fumarate in B. fragilis is proposed.