Biosynthesis of vitamin B12. Experiments with the anaerobe Eubacterium limosum and some labelled substrates

Determination of cobalamin and related compounds in foods

The microbiological assay of total cobalamin (vitamin B₁₂) by Lactobacillus delbrueckii subsp. lactis ATCC7830 is now used worldwide in food analysis because of its high sensitivity, low running cost, and no expensive instruments. It has been recently reported that some foods contain a substantial number of inactive corrinoid compounds, some of which are active in this bacterium. These results indicate that the microbiological method must be replaced with high-performance liquid chromatography or liquid chromatography/electrospray ionization-tandem mass spectrometry as there can specifically determine biologically active cobalamin. Nowadays, powerful tools, such as immunoaffinity columns, purify cobalamin simply and specifically. In this chapter, we summarized the determination methods of cobalamin and related compounds in foods. Various inactive corrinoids found in foods were also characterized.

CobT and BzaC catalyze the regiospecific activation and methylation of the 5-hydroxybenzimidazole lower ligand in anaerobic cobamide biosynthesis

Vitamin B12 and other cobamides are essential cofactors required by many organisms and are synthesized by a subset of prokaryotes via distinct aerobic and anaerobic routes. The anaerobic biosynthesis of 5,6-dimethylbenzimidazole (DMB), the lower ligand of vitamin B12, involves five reactions catalyzed by the bza operon gene products, namely the hydroxybenzimidazole synthase BzaAB/BzaF, phosphoribosyltransferase CobT, and three methyltransferases, BzaC, BzaD, and BzaE, that conduct three distinct methylation steps. Of these, the methyltransferases that contribute to benzimidazole lower ligand diversity in cobamides remain to be characterized, and the precise role of the bza operon protein CobT is unclear. In this study, we used the bza operon from the anaerobic bacterium Moorella thermoacetica (comprising bzaA-bzaB-cobT-bzaC) to examine the role of CobT and investigate the activity of the first methyltransferase, BzaC. We studied the phosphoribosylation catalyzed by MtCobT and found that it regiospecifically activates 5-hydroxybenzimidazole (5-OHBza) to form the 5-OHBza-ribotide (5-OHBza-RP) isomer as the sole product. Next, we characterized the domains of MtBzaC and reconstituted its methyltransferase activity with the predicted substrate 5-OHBza and with two alternative substrates, the MtCobT product 5-OHBza-RP and its riboside derivative 5-OHBza-R. Unexpectedly, we found that 5-OHBza-R is the most favored MtBzaC substrate. Our results collectively explain the long-standing observation that the attachment of the lower ligand in anaerobic cobamide biosynthesis is regiospecific. In conclusion, we validate MtBzaC as a SAM:hydroxybenzimidazole-riboside methyltransferase (HBIR-OMT). Finally, we propose a new pathway for the synthesis and activation of the benzimidazolyl lower ligand in anaerobic cobamide biosynthesis.

Sustained Dechlorination of Vinyl Chloride to Ethene in Dehalococcoides-Enriched Cultures Grown without Addition of Exogenous Vitamins and at Low pH

Trichloroethene (TCE) bioremediation has been demonstrated at field sites using microbial cultures harboring TCE-respiring Dehalococcoides whose growth is cobalamin (vitamin B₁₂)-dependent. Bioaugmentation cultures grown ex situ with ample exogenous vitamins and at neutral pH may become vitamin-limited or inhibited by acidic pH once injected into field sites, resulting in incomplete TCE dechlorination and accumulation of vinyl chloride (VC). Here, we report growth of the Dehalococcoides-containing bioaugmentation culture KB-1 in a TCE-amended mineral medium devoid of vitamins and in a VC-amended mineral medium at low pH (6.0 and 5.5). In these cultures, Acetobacterium, which can synthesize 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, and Sporomusa are dominant acetogens. At neutral pH, Acetobacterium supports complete TCE dechlorination by Dehalococcoides at millimolar levels with a substantial increase in cobalamin (∼20-fold). Sustained dechlorination of VC to ethene was achieved at pH as low as 5.5. Below pH 5.0, dechlorination was not stimulated by DMB supplementation but was restored by raising pH to neutral. Cell-extract assays revealed that vinyl chloride reductase activity declines significantly below pH 6.0 and is undetectable below pH 5.0. This study highlights the importance of cobamide-producing populations and pH in microbial dechlorinating communities for successful bioremediation at field sites.

Anaerobic biosynthesis of the lower ligand of vitamin B12

Vitamin B12 (cobalamin) is required by humans and other organisms for diverse metabolic processes, although only a subset of prokaryotes is capable of synthesizing B12 and other cobamide cofactors. The complete aerobic and anaerobic pathways for the de novo biosynthesis of B12 are known, with the exception of the steps leading to the anaerobic biosynthesis of the lower ligand, 5,6-dimethylbenzimidazole (DMB). Here, we report the identification and characterization of the complete pathway for anaerobic DMB biosynthesis. This pathway, identified in the obligate anaerobic bacterium Eubacterium limosum, is composed of five previously uncharacterized genes, bzaABCDE, that together direct DMB production when expressed in anaerobically cultured Escherichia coli. Expression of different combinations of the bza genes revealed that 5-hydroxybenzimidazole, 5-methoxybenzimidazole, and 5-methoxy-6-methylbenzimidazole, all of which are lower ligands of cobamides produced by other organisms, are intermediates in the pathway. The bza gene content of several bacterial and archaeal genomes is consistent with experimentally determined structures of the benzimidazoles produced by these organisms, indicating that these genes can be used to predict cobamide structure. The identification of the bza genes thus represents the last remaining unknown component of the biosynthetic pathway for not only B12 itself, but also for three other cobamide lower ligands whose biosynthesis was previously unknown. Given the importance of cobamides in environmental, industrial, and human-associated microbial metabolism, the ability to predict cobamide structure may lead to an improved ability to understand and manipulate microbial metabolism.

Physiological and molecular aspects of cobalamin transport

Minute doses of a complex cofactor cobalamin (Cbl, vitamin B12) are essential for metabolism. The nutritional chain for humans includes: (1) production of Cbl by bacteria in the intestinal tract of herbivores; (2) accumulation of the absorbed Cbl in animal tissues; (3) consumption of food of animal origin. Most biological sources contain both Cbl and its analogues, i.e. Cbl-resembling compounds physiologically inactive in animal cells. Selective assimilation of the true vitamin requires an interplay between three transporting proteins - haptocorrin (HC), intrinsic factor (IF), transcobalamin (TC) - and several receptors. HC is present in many biological fluids, including gastric juice, where it assists in disposal of analogues. Gastric IF selectively binds dietary Cbl and enters the intestinal cells via receptor-mediated endocytosis. Absorbed Cbl is transmitted to TC and delivered to the tissues with blood flow. The complex transport system guarantees a very efficient uptake of the vitamin, but failure at any link causes Cbl-deficiency. Early detection of a negative B12 balance is highly desirable to prevent irreversible neurological damages, anaemia and death in aggravated cases. The review focuses on the molecular mechanisms of cobalamin transport with emphasis on interaction of corrinoids with the specific proteins and protein-receptor recognition. The last section briefly describes practical aspects of recent basic research concerning early detection of B12-related disorders, medical application of Cbl-conjugates, and purification of corrinoids from biological samples.

Elucidating biosynthetic pathways for vitamins and cofactors

The elucidation of the pathways to the water-soluble vitamins and cofactors has provided many biochemical and chemical challenges. This is a reflection both of their complex chemical nature, and the fact that they are often made in small amounts, making detection of the enzyme activities and intermediates difficult. Here we present an orthogonal review of how these challenges have been overcome using a combination of methods, which are often ingenious. We make particular reference to some recent developments in the study of biotin, pantothenate, folate, pyridoxol, cobalamin, thiamine, riboflavin and molybdopterin biosynthesis.

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.

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.

Biosynthesis of vitamin B12 in anaerobic bacteria. Experiments with Eubacterium limosum on the incorporation of D-[1-13C]erythrose and [13C]formate into the 5,6-dimethylbenzimidazole moiety

Experiments on the incorporation of erythrose and formate into the 5,6-dimethylbenzimidazole moiety of vitamin B12 are described. In one experiment, a 1:1 mixture of D-[1-13C]erythrose and D-[1-13C]threose was added to a Eubacterium limosum fermentation. The vitamin B12 formed was methylated at N3 of its 5,6-dimethylbenzimidazole part and degraded to 1,5,6-trimethylbenzimidazole. The 13C-NMR spectrum of this compound exhibited a single prominent signal at 109.5 ppm due to 13C labeling in C7. This shows that C1 of erythrose or threose was originally incorporated exclusively into C4 of the 5,6-dimethylbenzimidazole moiety of vitamin B12. In another experiment, sodium [13C]formate was added to a culture of E. limosum. The vitamin B12 isolated was transformed into 1,5,6-trimethylbenzimidazole as before. The 13C-NMR spectrum also showed one prominent signal at 142.8 ppm, evoked by 13C at C2. These results demonstrate that erythrose is incorporated into the base part of vitamin B12 regiospecifically and that formate is the precursor of the C2.

The CobII and CobIII regions of the cobalamin (vitamin B12) biosynthetic operon of Salmonella typhimurium

A detailed deletion map of the CobII and CobIII regions of the cobalamin biosynthetic (cob) operon of Salmonella typhimurium LT2 has been constructed. The CobII region encodes functions needed for the synthesis of lower ligand 5,6-dimethylbenzimidazole (DMB); CobIII encodes functions needed for the synthesis of the nucleotide loop that joins DMB to the corrin macrocycle. The genetic analysis of 117 deletion, insertion, and point mutations indicates that (i) the CobII and CobIII mutations are contiguous--that is, they are grouped according to function; (ii) the CobII region is composed of four complementation groups (cobJKLM); (iii) cobM mutations do not complement mutations in any of the other three CobII groups; and (iv) CobIII mutations include three complementation groups that correspond to the cobU, cobS, and cobT genes.

5'-Methylbenzimidazolyl-cobamides are the corrinoids from some sulfate-reducing and sulfur-metabolizing bacteria

The sulfate-reducing bacteria Desulfobacterium autotrophicum, Desulfobulbus propionicus and Archaeoglobus fulgidus (VC-16) and the sulfur-metabolizing archaebacteria Desulfurolobus ambivalens and Thermoplasma acidophilum were found to contain considerable amounts of corrinoids, that were isolated and crystallized in their Co beta-cyano form. In three other sulfur-metabolizing archaebacteria, Thermoproteus neutrophilus, Pyrodictium occultum and Staphylothermus marinus significant amounts of corrinoids were not detected under the isolation methods used. The samples from the three sulfate-reducers were identified with Co alpha-[alpha-(5'-methylbenzimidazolyl)]-Co beta-cyanocobamide. This corrinoid was also obtained from a 5-methylbenzimidazole-supplemented Propionibacterium fermentation and was structurally characterized by ultraviolet/visible, CD, fast-atom-bombardment MS, 1H-and 13C-NMR spectroscopy. Also the major corrinoid from T. acidophilum was (tentatively) analyzed as a 5'-methylbenzimidazolyl-cobamide, whereas the main corrinoid from D. ambivalens was indicated to be vitamin B12 (a 5',6'-dimethylbenzimidazolyl-cobamide). The 5'-methylbenzimidazolylcobamides are found here as the common corrins of some sulfate-reducing and sulfur-metabolizing bacteria. The structural diversity due to the differing nucleotide bases of the corrins examined here and in methanogenic and acetogenic bacteria appears not to correlate to the biological function(s) of the corrins, but rather to be determined by biosynthetic properties of these organisms under natural growth conditions.

Biosynthesis of vitamin B-12 in anaerobic bacteria. Experiments with Eubacterium limosum and D-erythrose 14C-labeled in different positions

In anaerobic microorganisms the origin of C atoms 2 and 4-7 of the 5,6-dimethylbenzimidazole moiety of vitamin B-12 is still unknown. In order to tackle this problem we added several 14C-labeled putative precursors to Eubacterium limosum fermentations. The degradation of the isolated vitamin B-12 revealed that only D-erythrose, 14C-labeled in different positions, was efficiently incorporated into the 5,6-dimethylbenzimidazole part. The 5,6-dimethylbenzimidazole obtained from an experiment with D-[U-14C]erythrose was further degraded. It was found that C-2 was unlabeled, whereas half of the label was located in C-5 plus C-6, and the other half in C-4 plus C-7. These results demonstrate that in E. limosum D-erythrose is a precursor of C-atoms 4, 5, 6 and 7 of the 5,6-dimethylbenzimidazole part of vitamin B-12.

Biosynthesis of vitamin B-12 in anaerobic bacteria. Experiments with Eubacterium limosum on the origin of the amide groups of the corrin ring and of N-3 of the 5,6-dimethylbenzimidazole part

The pathway of vitamin B-12 biosynthesis in anaerobic bacteria differs in several respects from the pathway found in aerobic or aerotolerant microorganisms. The aim of this investigation was to elucidate the formation of the 5,6-dimethylbenzimidazole part and the amide groups of vitamin B-12 in anaerobic bacteria. [15N]Ammonium chloride or L-[amido-15N]glutamine or a mixture of [15N]ammonium sulfate and [15N]glycine was added to fermentations with Eubacterium limosum. The vitamin B-12 isolated from these fermentations was methylated and degraded to cobinamide and 1,5,6-trimethylbenzimidazole. The amide groups of cobinamide were hydrolyzed and the amide nitrogen of the side chains a, b, c, d, e and g trapped as benzamide. The 15N incorporation was determined by mass spectroscopy. Thus in the experiment with [15N]ammonium chloride the benzamide and the 1,5,6-trimethylbenzimidazole contained 9.6% 15N, whereas in the experiment with L-[amido-15N]glutamine 37.5% of the molecules were 15N labeled. The 1H-NMR spectrum of 1,5,6-trimethylbenzimidazole revealed that the 15N from the ammonium salts and from glutamine was incorporated into N-3 of the 5,6-dimethylbenzimidazole moiety of vitamin B-12. With a mixture of [15N]ammonium sulfate and [15N]glycine both nitrogens of 5,6-dimethylbenzimidazole became 15N-labeled. These experiments demonstrate that in E. limosum the amide nitrogen of glutamine is not only the precursor of the six amide groups of the corrin ring, but also of N-3 of the 5,6-dimethylbenzimidazole moiety of vitamin B-12.

Biosynthesis of vitamin B12. Different pathways in some aerobic and anaerobic microorganisms

Radioactivity from [1'-14C]riboflavin was incorporated into the 5,6-dimethylbenzimidazole moiety of Vitamin B12 in the aerobes Bacillus megaterium, Nocardia rugosa and Streptomyces sp. as well as in the aerotolerant anaerobe Propionibacterium freudenreichii, but not in the anaerobe Eubacterium limosum. As recently published for E. limosum, also in the anaerobe Clostridium barkeri radioactivity from [1-14C]glycine and [2-14C]glycine was found in the 5,6-dimethylbenzimidazole moiety, but not in the corrin moiety. The addition of L-[methyl-14C]methionine to C. barkeri led to the labeling of the corrin moiety and the 5,6-dimethylbenzimidazole moiety, showing that the seven "extra" methyl groups in the corrin ring as well as the two methyl groups of the base part originate from this precursor. In Clostridium thermoaceticum, forming the vitamin B12 analog 5-methoxybenzimidazolylcobamide, [1-14C]glycine and [2-14C]glycine were also incorporated into the 5-methoxybenzimidazole moiety, but not into the corrin ring. In E. limosum L-[U-14C]glutamate led to the labeling of the corrin ring of vitamin B12, but not of its base moiety. These results together with data from the literature indicate that a common biosynthetic pathway might exist for the corrinoid biosynthesis in aerobic microorganisms, and in those aerotolerant anaerobes like the Propionibacteria, which form the 5,6-dimethylbenzimidazole moiety of vitamin B12 only under aerobic conditions. They also show that this pathway differs from the pathway found in anaerobic bacteria.