Salmonella enterica synthesizes 5,6-dimethylbenzimidazolyl-(DMB)-α-riboside. Why some Firmicutes do not require the canonical DMB activation system to synthesize adenosylcobalamin

A cyanide-free sample preparation methodology prior to determination of vitamin B12 in infant milk formula using hydrophilic interaction liquid chromatography with fluorescence detection

The analysis of vitamin B12 in infant formulas typically requires the use of cyanide during sample preparation to convert the unstable vitamers (hydroxocobalamin, methylcobalamin and adenosylcobalamin) to cyanocobalamin, the most stable form of vitamin B12. To eliminate the risk to laboratory analysts in handling cyanide, alternative strategies are preferred for the analysis of vitamin B12. This research demonstrates the use of cobalamin-derived α-ribazole (a nucleoside moiety of vitamin B12) to determine total vitamin B12 content. Infant formula samples underwent protein denaturation and sugar removal with subsequent acidic hydrolysis and dephosphorylation employed to release α-ribazole, which was isolated by boronate affinity chromatography then analysed by hydrophilic interaction liquid chromatography with fluorescence detection. The method was validated using bovine- and ovine milk-based infant formula samples. The newly developed method was linear over the range of 0.65-6.48 ng mL-1 with repeatability of 3.78-5.47% relative standard deviation (RSDr, n = 10) and an intermediate precision of 3.59-10.0% RSDiR (n = 10). The limits of detection and quantitation (LOD and LOQ) were 0.4 and 1.2 μg 100 g-1 of dry weight, respectively. Accuracy was 68.9-76.4% and 68.7-80.0% at 50 and 150% of typical B12 concentrations in infant formula, respectively. The validated method was applied to eleven infant formulas and no statistical difference (p = 0.45, α = 0.05) was found when comparing with the results obtained using the AOAC Official Method 2014.02 high performance liquid chromatography with ultraviolet detection that requires the use of cyanide. These results indicate that the newly validated method is not only reliable but also offers a safer alternative for routine vitamin B12 determination in infant formula while maintaining high accuracy and precision.

The coenzyme B12 precursor 5,6-dimethylbenzimidazole is a flavin antagonist in Salmonella

Salmonella enterica subsp. enterica sv. Typhimurium str. LT2 (hereafter S. Typhimurium) synthesizes adenosylcobalamin (AdoCbl, CoB12) de novo only under anoxic conditions, but it can assemble the lower ligand loop (a.k.a. the nucleotide loop) and can form the unique C-Co bond present in CoB12 in the presence or absence of molecular oxygen. During studies of nucleotide loop assembly in S. Typhimurium, we noticed that the growth of this bacterium could be arrested by the lower ligand nucleobase, namely 5,6-dimethylbenzimidazole (DMB). Here we report in vitro and in vivo evidence that shows that the structural similarity of DMB to the isoalloxazine moiety of flavin cofactors causes its deleterious effect on cell growth. We studied DMB inhibition of the housekeeping flavin dehydrogenase (Fre) and three flavoenzymes that initiate the catabolism of tricarballylate, succinate or D-alanine in S. Typhimurium. Notably, while growth with tricarballylate was inhibited by 5-methyl-benzimidazole (5-Me-Bza) and DMB, growth with succinate or glycerol was arrested by DMB but not by 5-Me-Bza. Neither unsubstituted benzimidazole nor adenine inhibited growth of S. Typhimurium at DMB inhibitory concentrations. Whole genome sequencing analysis of spontaneous mutant strains that grew in the presence of inhibitory concentrations of DMB identified mutations effecting the cycA (encodes D-Ala/D-Ser transporter) and dctA (encodes dicarboxylate transporter) genes and in the coding sequence of the tricarballylate transporter (TcuC), suggesting that increased uptake of substrates relieved DMB inhibition. We discuss two possible mechanisms of inhibition by DMB.

A method for the isolation of α-ribazole from vitamin B12, and its enzymatic conversion to α-ribazole 5'-phosphate

Cobamides (Cbas) are the largest coenzymes known and are used by cells in all domains of life. These molecules are characterized by a central cobalt-containing tetrapyrrole ring with two opposing axial ligands on the α and β faces of the ring. All biologically active forms of Cbas have a 5'-deoxyadenosyl group as the upper (Coβ) ligand that is covalently attached to the cobalt ion of the ring. In contrast, the lower ligand is a nucleobase of diverse chemical structure; however, nucleobases are usually derivatives of benzimidazole or purine. Phenol and p-cresol can also serve as the nucleobase, but they cannot form a coordination bond with the cobalt ion of the ring because they lack a free pair of electrons. The Cba incorporating 5,6-dimethylbenzimidazole (DMB) is known as cobalamin (Cbl), and the coenzymic form of cobalamin is known as adenosylcobalamin (AdoCbl). A common vitamer of cobalamin has a cyano group as the upper ligand. This vitamer is known as cyanocobalamin (CNCbl), which is commercially marketed as vitamin B₁₂. Here, we describe a combination of chemical hydrolysis of cobalamin with the enzymatic dephosphorylation of the resulting α-R-3'-phosphate to yield α-R, which we enzymically convert to the pathway intermediate α-R-5'-phosphate (α-RP). The methods describe herein can be readily scaled up to generate large amounts of α-RP.

Cobamide remodeling

Cobamides are a family of structurally-diverse cofactors which includes vitamin B₁₂ and over a dozen natural analogs. Within the nucleotide loop structure, cobamide analogs have variable lower ligands that fall into three categories: benzimidazoles, purines, and phenols. The range of cobamide analogs that can be utilized by an organism is dependent on the specificity of its cobamide-dependent enzymes, and most bacteria are able to utilize multiple analogs but not all. Some bacteria have pathways for cobamide remodeling, a process in which imported cobamides are converted into compatible analogs. Here we discuss cobamide analog diversity and three pathways for cobamide remodeling, mediated by amidohydrolase CbiZ, phosphodiesterase CbiR, and some homologs of cobamide synthase CobS. Remodeling proteins exhibit varying degrees of specificity for cobamide substrates, reflecting different strategies to ensure that imported cobamides can be utilized.

Functional Studies of α-Riboside Activation by the α-Ribazole Kinase (CblS) from Geobacillus kaustophilus

We report the initial characterization of the α-ribazole (α-R) kinase enzyme of Geobacillus kaustophilus (GkCblS), which converts α-R to α-R-phosphate (α-RP) during the synthesis of cobamides. We implemented a continuous spectrophotometric assay to obtain kinetic parameters for several potential substrates and to study the specificity of the enzyme for α-N-linked ribosides. The apparent K_m values for α-R and ATP were 358 and 297 μM, respectively. We also report methods for synthesizing and quantifying non-commercially available α-ribosides and β-ribazole (β-R). Purified GkCblS activated α-R and other α-ribosides, including α-adenosine (α-Ado). GkCblS did not phosphorylate β-N-linked glycosides like β-adenosine or β-R. Expression of G. kaustophilus cblS⁺ in a Salmonella enterica subsp. enterica sv Typhimurium LT2 (S. enterica) strain lacking the nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyl transferase (CobT) enzyme resulted in the activation of various benzimidazole α-ribosides, and the synthesis of benzimidazolyl cobamides to levels that supported robust growth. Notably, α-Ado did not support growth under similar conditions, in spite of the fact that GkCblS phosphorylated α-Ado in vitro. When α-Ado was provided at a very high concentration, growth was observed. This result suggested that in S. enterica α-Ado transport may be inefficient. We conclude that GkCblS has specificity for α-N-glycosidic bonds, but not for the base in α-ribosides.

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.

Specificity of cobamide remodeling, uptake and utilization in Vibrio cholerae

Cobamides are a group of compounds including vitamin B₁₂ that can vary at the lower base position of the nucleotide loop. They are synthesized de novo by only a subset of prokaryotes, but some organisms encode partial biosynthesis pathways for converting one variant to another (remodeling) or completing biosynthesis from an intermediate (corrinoid salvaging). Here, we explore the cobamide specificity in Vibrio cholerae through examination of three natural variants representing major cobamide groups: commercially available cobalamin, and isolated pseudocobalamin and p-cresolylcobamide. We show that BtuB, the outer membrane corrinoid transporter, mediates the uptake of all three variants and the intermediate cobinamide. Our previous work suggested that V. cholerae could convert pseudocobalamin produced by cyanobacteria into cobalamin. In this work, cobamide specificity in V. cholerae is demonstrated by remodeling of pseudocobalamin and salvaging of cobinamide to produce cobalamin. Cobamide remodeling in V. cholerae is distinct from the canonical pathway requiring amidohydrolase CbiZ, and heterologous expression of V. cholerae CobS was sufficient for remodeling. Furthermore, function of V. cholerae cobamide-dependent methionine synthase MetH was robustly supported by cobalamin and p-cresolylcobamide, but not pseudocobalamin. Notably, the inability of V. cholerae to produce and utilize pseudocobalamin contrasts with enteric bacteria like Salmonella.

A New Class of Phosphoribosyltransferases Involved in Cobamide Biosynthesis Is Found in Methanogenic Archaea and Cyanobacteria

Cobamides are coenzymes used by cells from all domains of life but made de novo by only some bacteria and archaea. The last steps of the cobamide biosynthetic pathway activate the corrin ring and the lower ligand base, condense the activated intermediates, and dephosphorylate the product prior to the release of the biologically active coenzyme. In bacteria, a phosphoribosyltransferase (PRTase) enyzme activates the base into its α-mononucleotide. The enzyme from Salmonella enterica ( SeCobT) has been extensively biochemically and structurally characterized. The crystal structure of the putative PRTase from the archaeum Methanocaldococcus jannaschii ( MjCobT) is known, but its function has not been validated. Here we report the in vivo and in vitro characterization of MjCobT. In vivo, in vitro, and phylogenetic data reported here show that MjCobT belongs to a new class of NaMN-dependent PRTases. We also show that the Synechococcus sp. WH7803 CobT protein has PRTase activity in vivo. Lastly, results of isothermal titration calorimetry and analytical ultracentrifugation analysis show that the biologically active form of MjCobT is a dimer, not a trimer, as suggested by its crystal structure.

Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics

The vitamin B₁₂ family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria.

Novel Pathway for Corrinoid Compounds Production in Lactobacillus

Vitamin B₁₂ or cobalamin is an essential metabolite for humans, which makes it an interesting compound for many research groups that focus in different producer-strains synthesis pathways. In this work, we report the influence of key intermediaries for cobalamin synthesis added to the culture medium in two Lactobacillus (L.) strains, L. reuteri CRL 1098 and L. coryniformis CRL 1001. Here, we report that addition of Co²⁺ and 5,6-dimethylbenzimidazole increased the corrinoid compounds production in both strains while addition of L-threonine increased only the corrinoid compounds production by CRL 1001 strain. Then, we purified and characterized by LC-MS the corrinoid compounds obtained. Physiological studies besides in silico analysis revealed that L. reuteri CRL 1098 and L. coryniformis CRL 1001 follow different pathways for the last steps of the corrinoid compounds synthesis.

Facile isolation of α-ribazole from vitamin B12 hydrolysates using boronate affinity chromatography

Alpha-ribazole (α-R) is a unique riboside found in the nucleotide loop of coenzyme B₁₂ (CoB₁₂). α-R is not an intermediate of the de novo biosynthetic pathway of coenzyme B₁₂, but some bacteria of the phylum Firmicutes have evolved a two-protein system (transporter, kinase) that scavenges α-R from the environment and converts it to the pathway intermediate α-RP. Since α-R is not commercially available, one must either synthesize α-R, or isolate it from hydrolysates of vitamin B₁₂ (cyano-B₁₂, CNB₁₂), so the function of the above-mentioned proteins can be studied. Here we report a facile protocol for the isolation of α-R from CNB₁₂ hydrolysates. CNB₁₂ dissolved in NaOH (5 M) was heated to 85 °C for 75 min, then cooled to 4 °C for 30 min. The solution was neutralized with HCl (5 M), and the hydrolysate was diluted with an equal volume of ammonium acetate (0.3 M, pH 8.8). Alkaline phosphatase was added and the mixture was incubated at 37 °C for 16 h. After incubation, the sample was loaded onto a boronate affinity resin column, washed with ammonium sulfate (0.3 M, pH 8.8), water (to remove residual corrinoids) and finally with formic acid (0.1 M) to release (α-R). Formic acid was removed by lyophilization, and the final yield of α-R was 85% from the theoretically recoverable amount. Methods for quantifying the concentration of α-R are reported.