Biosynthesis of 5-hydroxybenzimidazolylcobamid (factor III) in Methanobacterium thermoautotrophicum

Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016

Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at 2.0 A resolution. VvRpiA is highly similar to Eschericihia coliRpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.

Studies of the CobA-type ATP:Co(I)rrinoid adenosyltransferase enzyme of Methanosarcina mazei strain Go1

Although methanogenic archaea use B(12) extensively as a methyl carrier for methanogenesis, little is known about B(12) metabolism in these prokaryotes or any other archaea. To improve our understanding of how B(12) metabolism differs between bacteria and archaea, the gene encoding the ATP:co(I)rrinoid adenosyltransferase in Methanosarcina mazei strain Gö1 (open reading frame MM3138, referred to as cobA(Mm) here) was cloned and used to restore coenzyme B(12) synthesis in a Salmonella enterica strain lacking the housekeeping CobA enzyme. cobA(Mm) protein was purified and its initial biochemical analysis performed. In vitro, the activity is enhanced 2.5-fold by the addition of Ca(2+) ions, but the activity was not enhanced by Mg(2+) and, unlike the S. enterica CobA enzyme, it was >50% inhibited by Mn(2+). The CobA(Mm) enzyme had a K(m)(ATP) of 3 microM and a K(m)(HOCbl) of 1 microM. Unlike the S. enterica enzyme, CobA(Mm) used cobalamin (Cbl) as a substrate better than cobinamide (Cbi; a Cbl precursor); the beta phosphate of ATP was required for binding to the enzyme. A striking difference between CobA(Se) and CobA(Mm) was the use of ADP as a substrate by CobA(Mm), suggesting an important role for the gamma phosphate of ATP in binding. The results from (31)P-nuclear magnetic resonance spectroscopy experiments showed that triphosphate (PPP(i)) is the reaction by-product; no cleavage of PPP(i) was observed, and the enzyme was only slightly inhibited by pyrophosphate (PP(i)). The data suggested substantial variations in ATP binding and probably corrinoid binding between CobA(Se) and CobA(Mm) enzymes.

Ribose-5-phosphate biosynthesis in Methanocaldococcus jannaschii occurs in the absence of a pentose-phosphate pathway

Recent work has raised a question as to the involvement of erythrose-4-phosphate, a product of the pentose phosphate pathway, in the metabolism of the methanogenic archaea (R. H. White, Biochemistry 43:7618-7627, 2004). To address the possible absence of erythrose-4-phosphate in Methanocaldococcus jannaschii, we have assayed cell extracts of this methanogen for the presence of this and other intermediates in the pentose phosphate pathway and have determined and compared the labeling patterns of sugar phosphates derived metabolically from [6,6-2H2]- and [U-13C]-labeled glucose-6-phosphate incubated with cell extracts. The results of this work have established the absence of pentose phosphate pathway intermediates erythrose-4-phosphate, xylose-5-phosphate, and sedoheptulose-7-phosphate in these cells and the presence of D-arabino-3-hexulose-6-phosphate, an intermediate in the ribulose monophosphate pathway. The labeling of the D-ara-bino-3-hexulose-6-phosphate, as well as the other sugar-Ps, indicates that this hexose-6-phosphate was the precursor to ribulose-5-phosphate that in turn was converted into ribose-5-phosphate by ribose-5-phosphate isomerase. Additional work has demonstrated that ribulose-5-phosphate is derived by the loss of formaldehyde from D-arabino-3-hexulose-6-phosphate, catalyzed by the protein product of the MJ1447 gene.

Retrobiosynthetic nuclear magnetic resonance analysis of amino acid biosynthesis and intermediary metabolism. Metabolic flux in developing maize kernels

Information on metabolic networks could provide the basis for the design of targets for metabolic engineering. To study metabolic flux in cereals, developing maize (Zea mays) kernels were grown in sterile culture on medium containing [U-(13)C(6)]glucose or [1,2-(13)C(2)]acetate. After growth, amino acids, lipids, and sitosterol were isolated from kernels as well as from the cobs, and their (13)C isotopomer compositions were determined by quantitative nuclear magnetic resonance spectroscopy. The highly specific labeling patterns were used to analyze the metabolic pathways leading to amino acids and the triterpene on a quantitative basis. The data show that serine is generated from phosphoglycerate, as well as from glycine. Lysine is formed entirely via the diaminopimelate pathway and sitosterol is synthesized entirely via the mevalonate route. The labeling data of amino acids and sitosterol were used to reconstruct the labeling patterns of key metabolic intermediates (e.g. acetyl-coenzyme A, pyruvate, phosphoenolpyruvate, erythrose 4-phosphate, and Rib 5-phosphate) that revealed quantitative information about carbon flux in the intermediary metabolism of developing maize kernels. Exogenous acetate served as an efficient precursor of sitosterol, as well as of amino acids of the aspartate and glutamate family; in comparison, metabolites formed in the plastidic compartments showed low acetate incorporation.

Identification of an alternative nucleoside triphosphate: 5'-deoxyadenosylcobinamide phosphate nucleotidyltransferase in Methanobacterium thermoautotrophicum delta H

Computer analysis of the archaeal genome databases failed to identify orthologues of all of the bacterial cobamide biosynthetic enzymes. Of particular interest was the lack of an orthologue of the bifunctional nucleoside triphosphate (NTP):5'-deoxyadenosylcobinamide kinase/GTP:adenosylcobinamide-phosphate guanylyltransferase enzyme (CobU in Salmonella enterica). This paper reports the identification of an archaeal gene encoding a new nucleotidyltransferase, which is proposed to be the nonorthologous replacement of the S. enterica cobU gene. The gene encoding this nucleotidyltransferase was identified using comparative genome analysis of the sequenced archaeal genomes. Orthologues of the gene encoding this activity are limited at present to members of the domain Archaea. The corresponding ORF open reading frame from Methanobacterium thermoautotrophicum Delta H (MTH1152; referred to as cobY) was amplified and cloned, and the CobY protein was expressed and purified from Escherichia coli as a hexahistidine-tagged fusion protein. This enzyme had GTP:adenosylcobinamide-phosphate guanylyltransferase activity but did not have the NTP:AdoCbi kinase activity associated with the CobU enzyme of S. enterica. NTP:adenosylcobinamide kinase activity was not detected in M. thermoautotrophicum Delta H cell extract, suggesting that this organism may not have this activity. The cobY gene complemented a cobU mutant of S. enterica grown under anaerobic conditions where growth of the cell depended on de novo adenosylcobalamin biosynthesis. cobY, however, failed to restore adenosylcobalamin biosynthesis in cobU mutants grown under aerobic conditions where de novo synthesis of this coenzyme was blocked, and growth of the cell depended on the assimilation of exogenous cobinamide. These data strongly support the proposal that the relevant cobinamide intermediates during de novo adenosylcobalamin biosynthesis are adenosylcobinamide-phosphate and adenosylcobinamide-GDP, not adenosylcobinamide. Therefore, NTP:adenosylcobinamide kinase activity is not required for de novo cobamide biosynthesis.

Retrobiosynthetic NMR studies with 13C-labeled glucose. Formation of gallic acid in plants and fungi

The biosynthesis of gallic acid was studied in cultures of the fungus Phycomyces blakesleeanus and in leaves of the tree Rhus typhina. Fungal cultures were grown with [1-13C]glucose or with a mixture of unlabeled glucose and [U-13C6]glucose. Young leaves of R. typhina were kept in an incubation chamber and were supplied with a solution containing a mixture of unlabeled glucose and [U-13C6]glucose via the leaf stem. Isotope distributions in isolated gallic acid and aromatic amino acids were analyzed by one-dimensional 1H and 13C NMR spectroscopy. A quantitative analysis of the complex isotopomer composition of metabolites was obtained by deconvolution of the 13C13C coupling multiplets using numerical simulation methods. This approach required the accurate analysis of heavy isotope chemical shift effects in a variety of different isotopomers and the analysis of long range 13C13C coupling constants. The resulting isotopomer patterns were interpreted using a retrobiosynthetic approach based on a comparison between the isotopomer patterns of gallic acid and tyrosine. The data show that both in the fungus and in the plant all carbon atoms of gallic acid are biosynthetically equivalent to carbon atoms of shikimate. Notably, the carboxylic group of gallic acid is derived from the carboxylic group of an early intermediate of the shikimate pathway and not from the side chain of phenylalanine or tyrosine. It follows that the committed precursor of gallic acid is an intermediate of the shikimate pathway prior to prephenate or arogenate, most probably 5-dehydroshikimate. A formation of gallic acid via phenylalanine, the lignin precursor, caffeic acid, or 3,4, 5-trihydroxycinnamic acid can be ruled out as major pathways in the fungus and in young leaves of R. typhina. The incorporation of uniformly 13C-labeled glucose followed by quantitative NMR analysis of isotopomer patterns is suggested as a general method for biosynthetic studies. As shown by the plant experiment, this approach is also applicable to systems with low incorporation rates.

Ribose biosynthesis and evidence for an alternative first step in the common aromatic amino acid pathway in Methanococcus maripaludis

An acetate-requiring mutant of Methanococcus maripaludis allowed efficient labeling of riboses following growth in minimal medium supplemented with [2-(13)C]acetate. Nuclear magnetic resonance and mass spectroscopic analysis of purified cytidine and uridine demonstrated that the C-1' of the ribose was about 67% enriched for 13C. This value was inconsistent with the formation of erythrose 4-phosphate (E4P) exclusively by the carboxylation of a triose. Instead, these results suggest that either (i) E4P is formed by both the nonoxidative pentose phosphate and triose carboxylation pathways or (ii) E4P is formed exclusively by the nonoxidative pentose phosphate pathway and is not a precursor of aromatic amino acids.

Heteronuclear NMR Studies of Cobalt Corrinoids. 18. Correlation of Structure and Magnetic Resonance Parameters in Base-On Cobalamins(1)

Recent X-ray crystal structure determinations (including a new X-ray determination of the structure of cyano-13-epicobalamin reported herein) create a series of seven base-on cobalamins structurally characterized by modern crystallographic techniques in which the intramolecular equilibrium constant for coordination of the axial benzimidazole ligand (Bzm) varies from 76.6 to 4.90 x 10(7). For the five normal, unepimerized cobalamins, the free energy change for this equilibrium correlates linearly with the axial Co-N bond length (r(2) = 0.99). Absolute assignment of the (1)H and (13)C NMR spectra of two of these structurally characterized cobalamins (CH(3)Cbl and CN-13-epiCbl) together with literature assignments for the other complexes now provides reliable (13)C NMR assignments and chemical shifts for all seven complexes. The magnetic anisotropies of the central cobalt atom of all seven complexes, estimated by a method described earlier, are well correlated with the axial Co-N bond distance (r(2) = 0.97) and the free energy of coordination of the Bzm ligand (r(2) = 0.95). The (31)P NMR chemical shift of the phosphodiester moiety of the nucleotide loop is excellently correlated to the axial Co-N bond length (r(2) = 0.996) of the unepimerized cobalamins and provides a reliable method of estimating this bond length. The (15)N chemical shifts of the axially coordinated Bzm nitrogen vary strongly with the axial Co-N bond distance and correlate linearly with this structural parameter (r(2) = 0.991) except for the case of H(2)OCbl(+), which deviates substantially. However, there is a good linear correlation (r(2) = 0.98) of this (15)N chemical shift with the free energy of Bzm coordination for the five unepimerized cobalamins. Attempts to correlate (13)C NMR chemical shifts with structural, thermodynamic, and corrin ring conformational parameters are discussed.

7-Azabenzimidazolylcobamide and 5,6-dimethyl-7-azabenzimidazolylcobamide, new vitamin B12-analogs synthesized from 4(5)-aminoimidazole by Eubacterium limosum

In anaerobic bacteria, glycine, formate, and the amide-N of glutamine are building blocks for the biosynthesis of the imidazole moiety of the vitamin B12-base 5,6-dimethylbenzimidazole. These building blocks are also used for the biosynthesis of the imidazole moiety of purine bases. Therefore we tested 4(5)-aminoimidazole, the base moiety of the purine nucleotide precursor 5-aminoimidazole ribonucleotide, for its putative function as precursor of 5,6-dimethylbenzimidazole. The anaerobic vitamin B12-producer Eubacterium limosum, grown in the presence of [2-13C]4(5)-aminoimidazole, synthesized nonlabeled vitamin B12, but also [2-13C]7-azabenzimidazolylcobamide and [2-13C]5,6-dimethyl-7-azabenzimidazolylcobamide. [2-13C]limidazole was used by E. limosum to form [2-13C]imidazolylcobamide. Simultaneously nonlabeled vitamin B12 was synthesized. This shows that 4(5)-aminoimidazole and imidazole are not intermediates in the biosynthesis of 5,6-dimethylbenzimidazole. However, 4(5)-aminoimidazole has obviously a structure similar to the structure of an as yet unknown precursor of the vitamin B12-base, and is therefore transformed into the aza analogs. In order to prepare a reference compound 4(5)-azabenzimidazole was added to a culture of Propionibacterium shermanii and to a culture of E. limosum, P. shermanil transformed this base mainly to 4-azabenzimidazolylcobamide, as determined by 1H NMR-spectroscopy (NOE experiment). In contrast E. limosum produced mainly 7-azabenzimidazolylcobamide. The reason for this difference is discussed.

Long-term culture of HepG2 hepatoma cells as a model for liver acute phase response during chronic inflammation. Effects of interleukin-6, dexamethasone and retinoic acid

HepG2 cells were cultured for 7 days in serum-free medium in the presence of interleukin-6 (IL-6), retinoic acid (RA) or dexamethasone (DX), and some plasma proteins secreted to the media were determined by electroimmunoassay whereas the contents of specific mRNAs in the cells was evaluated by Northern blot hybridization. Interleukin-6 maximally stimulated synthesis of alpha-1-antichymotrypsin between days 1 and 3 whereas the response of fibrinogen was delayed to days 3 to 7. Retinoic acid increased the effect of IL-6 on alpha-1-antichymotrypsin (ACT) and fibrinogen (FBG) on the level of both proteins and mRNAs. Synthesis of albumin was slightly inhibited by IL-6 and RA, and synthesis of transferrin was increased by RA but not by IL-6. Dexamethasone had small enhancing effect on the action of IL-6. These results suggest that long-term HepG2 cultures may provide an experimental model for liver acute phase response during chronic inflammation.

Pathway of glycogen metabolism in Methanococcus maripaludis

Methanococcus maripaludis, a facultatively autotrophic archaebacterium that grows with H2 or formate as the electron donor, does not assimilate sugars and other complex organic substrates. However, glycogen is biosynthesized intracellularly and commonly reaches values of 0.34% of the cellular dry weight in the early stationary phase. To determine the pathway of glycogen catabolism, specific enzymes of sugar metabolism were assayed in cell extracts. The following enzymes were found (specific activity in milliunits per milligram of protein): glycogen phosphorylase, 4.4; phosphoglucomutase, 10; glucose-6-phosphate isomerase, 9; 6-phosphofructokinase, 5.6, fructose-1,6-bisphosphatase, 10; fructose-1,6-bisphosphate aldolase, 4.2; triosephosphate isomerase, 44; glyceraldehyde-3-phosphate dehydrogenase, 26; phosphoglycerate kinase, 20; phosphoglycerate mutase, 78; enolase, 107; and pyruvate kinase, 4.0. Glyceraldehyde-3-phosphate dehydrogenase was NADP+ dependent, and the pyruvate kinase required MnCl2. The 6-phosphofructokinase had an unusually low pH optimum of 6.0. Four nonoxidative pentose-biosynthetic enzymes were found (specific activity in milliunits per milligram of protein): transketolase, 12; transaldolase, 24; ribulose-5-phosphate-3-epimerase, 55; and ribulose-5-phosphate isomerase, 100. However, the key enzymes of the oxidative pentose phosphate pathway, the reductive pentose phosphate pathway, and the classical and modified Entner-Duodoroff pathways were not detected. Thus, glycogen appears to be catabolized by the Embden-Meyerhoff-Parnas pathway. This result is in striking contrast to the nonmethanogenic archaebacteria that have been examined, among which the Entner-Doudoroff pathway is common. A dithiothreitol-specific NADP(+)-reducing activity was also found (8.5 mU/mg of protein). Other thiol compounds, such as cysteine hydrochloride, reduced glutathione, and 2-mercaptoethanesulfonic acid, did not replace dithiothreitol for this activity. The physiological significance of this activity is not known.

Biosynthesis of vitamin B12 in anaerobic bacteria. Transformation of 5-hydroxybenzimidazole and 5-hydroxy-6-methylbenzimidazole into 5,6-dimethylbenzimidazole in Eubacterium limosum

Eubacterium limosum transformed [2-13C]5-hydroxybenzimidazole not only into [2-13C]5-hydroxybenzimidazolylcobamide, but also into [2-13C]5-methoxy-6-methylbenzimidazolylcobamide and into [2-13C]5,6-dimethylbenzimidazolylcobamide (vitamin B12). [2-13C]5-Hydroxy-6-methyl-benzimidazole was used by this bacterium to form [2-13C]5-hydroxy-6-methylbenzimidazolyl-cobamide, [2-13C]5-methoxy-6-methylbenzimidazolylcobamide and [2-13C]5,6-dimethylbenzimidazolylcobamide. The 1H-NMR spectrum of the 5,6-dimethylbenzimidazole isolated from the 13C-labeled vitamin B12 preparations revealed that the externally added bases had been transformed into the vitamin B12 base almost without dilution of the label. This suggests that 5-hydroxybenzimidazole and 5-hydroxy-6-methylbenzimidazole are precursors of 5,6-dimethylbenzimidazole. On the basis of these results, a hypothetical scheme for the biosynthesis of 5,6-dimethylbenzimidazole via 5-hydroxybenzimidazole and 5-hydroxy-6-methylbenzimidazole is discussed. This scheme can also explain the formation of the other benzimidazole bases found in natural vitamin B12 analogs.