Structure of the Ni/Fe-S protein subcomponent of the acetyl-CoA decarbonylase/synthase complex from Methanosarcina thermophila at 26-A resolution.

The acetyl-CoA decarbonylase/synthase (ACDS) complex is responsible for synthesis and cleavage of acetyl-CoA in methanogens. The complex is composed of five different subunits, with a probable stoichiometry of alpha(8)beta(8)gamma(8)delta(8)epsilon(8). The native molecular mass of a subcomponent of the ACDS complex from Methanosarcina thermophila, the Ni/Fe-S protein containing the 90-kDa alpha and 19-kDa epsilon subunits, was determined by scanning transmission electron microscopy. A value of 218.6 +/- 19.6 kDa (n = 566) was obtained, thus establishing that the oligomeric structure of this subcomponent is alpha(2)epsilon(2). The three-dimensional structure of alpha(2)epsilon(2) was determined at 26-A resolution by analysis of a large number of electron microscopic images of negatively stained, randomly oriented particles. The alpha(2)epsilon(2) subcomponent has a globular appearance, 110 A in diameter, and consists of two large, hemisphere-like masses that surround a hollow internal cavity. The two large masses are connected along one face by a bridge-like structure and have relatively less protein density joining them at other positions. The internal cavity has four main openings to the outside, one of which is directly adjacent to the bridge. The results are consistent with a structure in which the large hemispheric masses are assigned to the two alpha subunits, with epsilon(2) as the bridge forming a structural link between them. The structure of the alpha(2)epsilon(2) subcomponent is discussed in connection with biochemical data from gel filtration, crosslinking, and dissociation experiments and in the context of its function as a major component of the ACDS complex.

Iron acquisition in plague: modular logic in enzymatic biogenesis of yersiniabactin by Yersinia pestis.

BACKGROUND: Virulence in the pathogenic bacterium Yersinia pestis, causative agent of bubonic plague, has been correlated with the biosynthesis and transport of an iron-chelating siderophore, yersiniabactin, which is induced under iron-starvation conditions. Initial DNA sequencing suggested that this system is highly conserved among the pathogenic Yersinia. Yersiniabactin contains a phenolic group and three five-membered thiazole heterocycles that serve as iron ligands. RESULTS: The entire Y. pestis yersiniabactin region has been sequenced. Sequence analysis of yersiniabactin biosynthetic regions (irp2-ybtE and ybtS) reveals a strategy for siderophore production using a mixed polyketide synthase/nonribosomal peptide synthetase complex formed between HMWP1 and HMWP2 (encoded by irp1 and irp2). The complex contains 16 domains, five of them variants of phosphopantetheine-modified peptidyl carrier protein or acyl carrier protein domains. HMWP1 and HMWP2 also contain methyltransferase and heterocyclization domains. Mutating ybtS revealed that this gene encodes a protein essential for yersiniabactin synthesis. CONCLUSIONS: The HMWP1 and HMWP2 domain organization suggests that the yersiniabactin siderophore is assembled in a modular fashion, in which a series of covalent intermediates are passed from the amino terminus of HMWP2 to the carboxyl terminus of HMWP1. Biosynthetic labeling studies indicate that the three yersiniabactin methyl moieties are donated by S-adenosylmethionine and that the linker between the thiazoline and thiazolidine rings is derived from malonyl-CoA. The salicylate moiety is probably synthesized using the aromatic amino-acid biosynthetic pathway, the final step of which converts chorismate to salicylate. YbtS might be necessary for converting chorismate to salicylate.

Redox-dependent acetyl transfer partial reaction of the acetyl-CoA decarbonylase/synthase complex: kinetics and mechanism.

Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex that plays a central role in energy metabolism in Methanosarcina barkeri grown on acetate. The ACDS complex carries out an unusual reaction involving net cleavage of the acetyl C-C and thioester bonds of acetyl-CoA. The overall reaction is composed of several partial reactions, one of which involves catalysis of acetyl group transfer. To gain insight into the overall reaction, a study was carried out on the kinetics and mechanism of the acetyltransferase partial reaction. Analysis by HPLC was used to quantify rates of acetyl transfer from acetyl-CoA both to 3'-dephospho-CoA and, by isotope exchange, to 14C-labeled CoA. Acetyl transfer activity was observed only under strongly reducing conditions, and was half-maximal at -486 mV at pH 6.5. The midpoint activation potential became increasingly more negative as the pH was increased, indicating the involvement of a protonation step. Cooperative dependence on acetyl-CoA concentration was exhibited in reactions that contained incompletely reduced enzyme; however, under redox conditions supporting maximum activity, hyperbolic kinetics were found. A ping-pong steady state kinetic mechanism was established, consistent with formation of an acetyl-enzyme intermediate. Analysis of the inhibitory effects of CoA on acetyl transfer to 3'-dephospho-CoA provided values for KiCoA of 6.8 microM and for Kiacetyl-CoA of 45 microM; isotope exchange analyses yielded values of 32 and 120 microM, respectively. Two separate measures of stability yielded values for the free energy of hydrolysis of the acetyl-enzyme intermediate of -9.6 and -9.3 kcal/mol, an indication of a high-energy bonding interaction in the acetyl-enzyme species. Implications for the mechanism of C-C bond cleavage are discussed.

Loop III region of platelet-derived growth factor (PDGF) B-chain mediates binding to PDGF receptors and heparin.

Site-directed mutagenesis of the platelet-derived growth factor (PDGF) B-chain was conducted to determine the importance of cationic amino acid residues (Arg160-Lys161-Lys162; RKK) located within the loop III region in mediating the biological and cell-association properties of the molecule. Binding to both PDGF alpha-and beta-receptors was inhibited by the conversion of all three cationic residues into anionic glutamates (RKK-->EEE), whereas an RKK-->SSS mutant also exhibited a modest loss in affinity for beta-receptors. Replacements with serine at either Arg160 (RKK-->SKK) or at all three positions (RKK-->SSS) had little effect on binding to alpha-receptors. Replacements with either glutamic or serine residues at any of the three positions also resulted in significant inhibition of heparin-binding activity. Furthermore, the RKK-->EEE mutant exhibited decreased association with the cell surface and accumulated in the culture medium as 29-32 kDa forms. Stable transfection of U87 astrocytoma cells with RKK-->EEE mutants of either the A-chain or the B-chain inhibited malignant growth in athymic nude mice. Despite altered receptor-binding activities, each of the loop III mutants retained full mitogenic activity when applied to cultured Swiss 3T3 cells. CD spectrophotometric analysis of the RKK-->EEE mutant revealed a secondary structure indistinguishable from the wild type, with a high degree of beta-sheet structure and random coil content (50% and 43% respectively). These findings indicate an important role of the Arg160-Lys161-Lys162 sequence in mediating the biological and cell-associative activities of the PDGF-BB homodimer, and reveal that the mitogenic activity of PDGF-BB is insufficient to mediate its full oncogenic properties.

Acetyl-CoA decarbonylase/synthase complex from Archaeoglobus fulgidus.

The acetyl-CoA decarbonylase/synthase (ACDS) multienzyme complex catalyzes the reversible cleavage and synthesis of acetyl-CoA in methanogens. This report of the enzyme complex in Archaeoglobus fulgidus demonstrates the existence of a functional ACDS complex in an organism that is not a methanogen. The A. fulgidus enzyme complex contained five subunits of 89, 72, 50, 49.5, and 18.5 kDa, and it catalyzed the overall synthesis of acetyl-CoA according to the following reaction: CO2 + 2 Fdred(Fe2+) + 2 H+ + CH3 - H4SPt + CoA <==> acetyl-CoA + H4SPt + 2 Fdox(Fe3+) + H2O where Fd is ferredoxin, and CH3-H4SPt and H4SPt denote N5-methyl-tetrahydrosarcinapterin and tetrahydrosarcinapterin, respectively.

Partial reactions catalyzed by protein components of the acetyl-CoA decarbonylase synthase enzyme complex from Methanosarcina barkeri.

In methanogens, the acetyl-CoA decarbonylase synthase (ACDS) complex, which has five different subunits, catalyzes synthesis and cleavage of acetyl-CoA according to the reaction: CO2 + 2H+ + 2e- + CH3-H4SPt + CoA <--> acetyl-CoA + H4SPt + H2O, where H4SPt and CH3-H4SPt are tetrahydrosarcinapterin and N5-methyl-tetrahydrosarcinapterin, respectively. We have dissociated the ACDS complex into three protein components by limited proteolytic digestion. Catalysis of acetyl-CoA synthesis was lost in parallel with the loss of the intact beta subunit; however, no decrease in activity was detected in any of three partial reactions found to be catalyzed by distinct protein components of the proteolyzed ACDS complex: (a) CO dehydrogenase, catalyzed by the alpha epsilon component, (b) CH3-H4pteridine:cob(I)amide-protein methyltransferase, catalyzed by the intact gamma subunit and fragments of the delta subunit, and (c) acetyltransferase, catalyzed by a truncated form of the beta subunit. The results indicated that the beta subunit is responsible for binding CoA and acetyl-CoA and suggested that acetyl-enzyme formation occurs on the beta subunit. A value of 5.5 x [H+]-1 M-1 was determined for the equilibrium constant of the following reaction at pH 7.5 and 25 degrees C: CH3-H4SPt + cob(I)amide-protein + H+ <--> H4SPt + CH3-cob(III)amide-protein.

Reactivity of a paramagnetic enzyme--CO adduct in acetyl-CoA synthesis and cleavage.

Partial reactions of acetyl-CoA cleavage by the Methanosarcina barkeri acetyl-CoA decarbonylase synthase enzyme complex were investigated by UV--visible and electron paramagnetic resonance (EPR) spectroscopy. Reaction of the enzyme complex with carbon monoxide generated an EPR-detectable adduct with principal g values of 2.089, 2.076, and 2.028, and line widths of 13.76, 16.65, and 5.41 G, respectively. The EPR signal intensity was dependent upon both enzyme and carbon monoxide concentration. A second signal with gav = 2.050 was generated by storage of the CO-exposed enzyme for 17 months at -70 degrees C. Reaction of the enzyme complex with low levels of CO caused reduction of the enzyme complex, but did not result in immediate formation of the NiFeC signal (designated NiFeC based on isotopic substitution studies carried out by others in analogous systems from Clostridium thermoaceticum and Methanosarcina thermophila). Further addition of CO generated the NiFeC signal, and the signal amplitude then increased progressively with increasing CO concentration. UV-visible spectra showed that enzyme Fe-S and corrinoid centers were already fully reduced at levels of CO significantly lower than needed for maximal EPR signal intensity. This result indicated that the EPR signal is formed by reaction of the reduced enzyme with CO (or a reduced one-carbon species), rather than with a one-carbon unit at the oxidation level of CO2. Addition of coenzyme A, acetyl-CoA, or tetrahydrosarcinapterin had no effect on the EPR signal. In contrast, addition of N5-methyltetrahydrosarcinapterin (CH3-H4SPt) abolished the EPR signal. EPR spectra recorded at 20-21 K revealed that reaction with CH3-H4SPt affects only the enzyme NiFeC signal, and does not influence other EPR-detectable Fe-S center(s). The results suggest that the enzyme--CO adduct reacts with CH3-H4SPt to form an EPR-silent enzyme-acetyl species. Preincubation of the enzyme complex with CO and CH3-H4SPt, both of which were required, produced an approximately 44-fold increase in the turnover rate of acetyl-CoA synthesis. The relevance of these findings to mechanisms involving possible reductive methylation of the enzyme and/or acetyl-enzyme formation is discussed.

Characterization of human T-cell responses to Yersinia enterocolitica superantigen.

We reported that antigenic preparations from Yersinia enterocolitica stimulate murine T cells in a manner consistent with that of superantigens. As a consequence we examined whether Y. enterocolitica antigenic preparations stimulate human T-cell cultures. Human T cells, enriched from peripheral blood lymphocytes, were stimulated to proliferate in the presence of Y. enterocolitica cytoplasmic and membrane preparations. This activity has also been shown to be sensitive to protease treatment, indicating the presence of a protein, and when separated by ion-exchange chromatography a single peak of activity is resolved. Furthermore, this proliferation was inhibited, in a dose-dependent manner, by the presence of antibodies directed against MHC class II antigens, indicating a requirement for these molecules. When these cells were stained with a panel of V beta-specific antibodies to determine if there was an enrichment of a particular V beta-bearing T-cell subset after stimulation, results indicate a significant enrichment of T cells bearing V beta 3, V beta 12, V beta 14, and V beta 17 over controls. Taken together, these data are consistent with a Y. enterocolitica product acting as a superantigen for human T cells.

Substrate and accessory protein requirements and thermodynamics of acetyl-CoA synthesis and cleavage in Methanosarcina barkeri.

Enzymological studies on the multienzyme acetyl-CoA decarbonylase synthase (ACDS) complex from Methanosarcina barkeri have been conducted in order to identify and characterize physiologically relevant substrates and reactions in acetyl-CoA synthesis and decomposition in methanogens. Whereas previous investigations employed carbon monoxide as substrate and reducing agent for acetyl-CoA synthesis, we discovered that bicarbonate (or CO2) acts as a highly efficient carbonyl group precursor substrate in the presence of either hydrogen or Ti3+.EDTA as reducing agent. In reactions with Ti3+.EDTA, synthesis of acetyl-CoA was strongly dependent on ferredoxin, and in reactions with H2, dependence on ferredoxin was absolute. Two major hydrogenases were resolved from the enzyme complex preparation by HPLC gel filtration. One of these hydrogenases was shown to be active in reconstitution of acetyl-CoA synthesis in CO2-containing reactions with H2 as reducing agent. The hydrogenase active in reconstitution was capable of reducing ferredoxin, but was unreactive toward the 8-hydroxy-5-deazaflavin derivative coenzyme F420. In contrast, the hydrogenase that did not reconstitute acetyl-CoA synthesis was reactive with F420 but was unable to reduce ferredoxin. Further experiments were performed in which the value of the equilibrium constant (Keq) was determined for the reaction: H2 + CO2 + CH3-H4SPt + CoASH <--> acetyl-CoA + H4SPt + H2O, where CH3-H4SPt and H4SPt stand for N5-methyl-tetrahydrosarcinapterin and tetrahydrosarcinapterin, respectively. Keq for this reaction was found to be 2.09 x 10(6) M-1ATMH2-1 at 37 degrees C. Calculations of thermodynamic values for additional, related reactions were made and are discussed.(ABSTRACT TRUNCATED AT 250 WORDS)

Biosynthesis of biotin from dethiobiotin by the biotin auxotroph Lactobacillus plantarum.

Lactobacillus plantarum requires biotin for growth. We show that in the presence of high levels of the biotin biosynthetic precursor, dethiobiotin, L. plantarum synthesizes biotin and grows in medium with dethiobiotin but without biotin. Lactobacillus casei also grew under similar conditions.

Purine metabolism in Methanococcus vannielii.

Methanococcus vannielii is capable of degrading purines to the extent that each of these purines may serve as the sole nitrogen source for growth. Results presented here demonstrate that purine degradation by M. vannielii is accomplished by a route similar to that described for clostridia. Various characteristics of the purine-degrading pathway of M. vannielii are described. Additionally, it is shown that M. vannielii does not extensively degrade exogenously supplied guanine if that compound is present at levels near or lower than those required to supply the cellular guanine requirement. Under those conditions, M. vannielii incorporates the intact guanine molecule into its guanine nucleotide pool. The benefits of a purine-degrading pathway to methanogens are discussed.

Purification and properties of carbon monoxide dehydrogenase from Methanococcus vannielii.

Carbon monoxide dehydrogenase was purified to homogeneity from Methanococcus vannielii grown with formate as the sole carbon source. The enzyme is composed of subunits with molecular weights of 89,000 and 21,000 in an alpha 2 beta 2 oligomeric structure. The native molecular weight of carbon monoxide dehydrogenase, determined by gel electrophoresis, is 220,000. The enzyme from M. vannielii contains 2 g-atoms of nickel per mol of enzyme. Except for its relatively high pH optimum of 10.5 and its slightly greater net positive charge, the enzyme from M. vannielii closely resembles carbon monoxide dehydrogenase isolated previously from acetate-grown Methanosarcina barkeri. Carbon monoxide dehydrogenase from M. vannielii constitutes 0.2% of the soluble protein of the cell. By comparison the enzyme comprises 5% of the soluble protein in acetate-grown cells of M. barkeri and approximately 1% in methanol-grown cells.

Conversion of purines to xanthine by Methanococcus vannielii.

Based on the finding that Methanococcus vannielii can employ any of several purines as the sole nitrogen source, an investigation was undertaken to elucidate the pathways of purine metabolism in this organism. Cell-free extracts of M. vannielii converted guanine, uric acid, and hypoxanthine to xanthine and also formed guanine from guanine nucleotides or guanosine. The conversions of guanine and uric acid to xanthine appear to occur by pathways similar to those described in clostridia. The conversion of hypoxanthine to xanthine, however, is different than that described for Clostridium cylindrosporum and C. acidiurici, but is similar to that of C. purinolyticum, and apparently involves the direct oxidation of hypoxanthine to xanthine.

Assay for biotin in the presence of dethiobiotin with Lactobacillus plantarum.

At concentrations greater than approximately 0.5 microM, dethiobiotin can cause the bioassay for biotin, which employs Lactobacillus plantarum, to over value the actual biotin level. This can be as much as 30-fold at 10 microM DL-dethiobiotin and 5 pM biotin. Dethiobiotin does this by exerting a sparing effect on the biotin response by the assay organism. We demonstrate one way to determine the actual biotin concentration in the presence of interfering levels of dethiobiotin.

Utilization of purines or pyrimidines as the sole nitrogen source by Methanococcus vannielii.

Studies of biosynthetic pathways with purines as substrates showed that Methanococcus vannielii was capable of degrading xanthine to an extent that several of the carbon atoms were converted to CO2. Experiments to determine whether this catabolic activity could satisfy the entire nitrogen requirement for growth of M. vannielii showed that urate, guanine, xanthine, or hypoxanthine, but not adenine, could serve as the sole nitrogen source. The pyrimidines uracil and thymine, but not cytosine, were also degraded to serve as a source of nitrogen. Although urate was extensively degraded, it did not replace formate as the sole carbon source for growth of M. vannielii under the conditions imposed.

Determination of the metabolic origin of the sulfur atom in thiamin of Escherichia coli by mass spectrometry.

In this study cells were grown in 34S-sulfate or L-[sulfane-34S]thiocystine, and the effects of unlabeled methionine and cystine on incorporation of sulfur into methionine, cystine and thiamin were determined. Unlabeled methionine effectively suppresses the incorporation of 34S into methionine but not into cysteine or thiamin. In contrast, cystine blocks incorporation of 34S only to approximately the relative ratio of 32S to 34S indicating, that cysteine is closely related to the origin of the sulfur in thiamin, and therefore the sulfane sulfur of thiocystine is also an effective source of the thiamin sulfur.

Determination of the metabolic origins of the sulfur and 3'-nitrogen atoms in biotin of Escherichia coli by mass spectrometry.

Two steps in the biosynthesis of biotin in Escherichia coli, incorporation of the nitrogen atom of methionine into 7-keto-8-aminopelargonic acid and of the sulfur atom into dethiobiotin, were examined. Sulfur and nitrogen metabolism were monitored by gas chromatography-mass spectrometry of volatile derivatives of internal (protein-bound) amino acids and excreted biotin. We were able to show that internal cysteine and excreted biotin were labeled to the same extent with 34S from either of two exogenous sulfur sources, 34SO4(2)-or L-[sulfane-34S]thiocystine. Internal methionine was eliminated from consideration, while cysteine, or possibly a closely related intermediate, was implicated as providing the sulfur atom for biotin biosynthesis. Also, in experiments designed to follow the metabolism of the nitrogen atom of methionine, it was found that biotin excreted into the culture medium by this organism grown with 95 atom % [15N]methionine contained greater than 70 atom % excess 15N in one of the nitrogens over that obtained from cultures grown with methionine of natural abundance 15N. These results provide evidence for the direct transfer of the methionine nitrogen as the role of S-adenosylmethionine in the conversion of 7-keto-8-aminopelargonic acid to 7,8-diaminopelargonic acid.

The origin of sulfur in biotin.

The comparative ability of Escherichia coli K-12 hpb lambda-, a biotin overproducing strain, to incorporate 35S from isotopically labeled L-methionine, L-cystine, and the sulfane sulfur of thiocystine was determined. Comparison of the specific activity of sulfur in biotin produced by the organism with that of the 35S-labeled amino acids demonstrates that the sulfur of cystine is transferred to biotin with an efficiency of at least 75%, that the sulfur of methionine does not contribute to biotin significantly, and that the sulfane sulfur of thiocystine contributes approximately one-third of the sulfur to newly synthesized biotin and is essentially equivalent in utilization to that of the other two sulfur atoms in the molecule.