Molecular cloning, expression and characterization of pyridoxamine-pyruvate aminotransferase

The PdxR-PdxKU locus involved in vitamin B6 salvage is important for group A streptococcal resistance to neutrophil killing and survival in human blood

Streptococcus pyogenes (Group A Streptococcus, GAS) is a Gram-positive bacterium that inflicts both superficial and life-threatening diseases on its human host. Analysis of fitness using a transposon mutant library revealed that genes predicted to be involved in vitamin B6 acquisition are associated with fitness in whole human blood. Vitamin B6 is essential for all life and is important for many cellular functions. In several streptococcal species, it has been shown that mutants in B6 acquisition exhibited reduced virulence phenotypes and were attenuated during infection. In GAS, B6 acquisition is believed to be controlled by the pdxR-pdxKU locus, where PdxR is a positive regulator of pdxKU, which encodes for a B6-substrate kinase and permease, respectively. Mutants in the regulator (ΔpdxR) and salvage machinery (ΔpdxKU) both exhibited modest growth defects when grown in oxygenated conditions with limited vitamin B6 precursors. ∆pdxR and ∆pdxKU mutants also exhibited an impaired ability to survive when challenged with whole human or mouse blood. This defect was characterized by reduced survival in the presence of human neutrophil-like HL60s, primary polymorphonuclear leukocytes, and antimicrobial peptide LL-37. Promoter analysis showed that PdxR is an autoregulator and activated pdxKU in the absence of B6. Interestingly, ∆pdxR and ∆pdxKU mutants were not attenuated in mouse models of infection, suggesting a species-specific impact on virulence. Overall, it appears that pdxR-pdxKU is associated with GAS vitamin B6 metabolism as well as pathogen survival during encounters with the human innate immune system.IMPORTANCEBacterial pathogens such as Streptococcus pyogenes (Group A Streptococcus, GAS) must be able to obtain needed nutrients in their human host. Vitamin B6 or pyridoxal 5' phosphate is essential for all life and is important for many cellular functions. In other streptococcal pathogens, B6 acquisition has been shown to be important for their ability to cause disease. Here, we show that loss of the putative vitamin B6 salvage pathway locus pdxR-pdxKU affects GAS pathogenesis when encountering innate immune responses from phagocytic neutrophils and antimicrobial peptides within the host. pdxR-pdxKU may contribute to oxygen tolerance through B6; however, there appear to be other mechanisms for salvaging vitamin B6. Overall, pdxR-pdxKU is associated with GAS resistance to the human innate immune response and oxygen tolerance and contributes modestly to B6 metabolism.

Evolutionary Origin and Functional Diversification of Aminotransferases

Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.

A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis

The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD⁺ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.

Bioconversion of pyridoxine to pyridoxamine through pyridoxal using a Rhodococcus expression system

Pyridoxamine, which is a form of vitamin B₆, is a promising candidate for a prophylactic and/or remedy for diabetic complications. Pyridoxamine is chemically synthesized by an oxidative method in manufacturing. However, pyridoxamine production by bioconversion, which is generally preferable for environmental and energetic aspects, has been little investigated. Therefore, I aimed to produce pyridoxamine from pyridoxine, which is a readily and economically available starting material, by bioconversion using a Rhodococcus expression system. I found in the bioconversion of pyridoxine to pyridoxal, approximately 450 mM pyridoxal was produced from 500 mM pyridoxine using recombinant Rhodococcus erythropolis expressing the pyridoxine 4-oxidase gene derived from Mesorhizobium loti. Next, in the bioconversion of pyridoxal to pyridoxamine using recombinant R. erythropolis expressing the pyridoxamine-pyruvate aminotransferase gene derived from M. loti, the bioconversion rate was approximately 80% under the same conditions as pyridoxal production. Finally, in the bioconversion of pyridoxine to pyridoxamine through pyridoxal using recombinant R. erythropolis coexpressing the genes for pyridoxine 4-oxidase and pyridoxamine-pyruvate aminotransferase, the bioconversion rate was approximately 75%. Based on these findings, pyridoxamine production by bioconversion using a Rhodococcus expression system may be of interest for future industrial applications.

Vitamin B6 metabolism in microbes and approaches for fermentative production

Vitamin B6 is a designation for the six vitamers pyridoxal, pyridoxine, pyridoxamine, pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate, and pyridoxamine. PLP, being the most important B6 vitamer, serves as a cofactor for many proteins and enzymes. In contrast to other organisms, animals and humans have to ingest vitamin B6 with their food. Several disorders are associated with vitamin B6 deficiency. Moreover, pharmaceuticals interfere with metabolism of the cofactor, which also results in vitamin B6 deficiency. Therefore, vitamin B6 is a valuable compound for the pharmaceutical and the food industry. Although vitamin B6 is currently chemically synthesized, there is considerable interest on the industrial side to shift from chemical processes to sustainable fermentation technologies. Here, we review recent findings regarding biosynthesis and homeostasis of vitamin B6 and describe the approaches that have been made in the past to develop microbial production processes. Moreover, we will describe novel routes for vitamin B6 biosynthesis and discuss their potential for engineering bacteria that overproduce the commercially valuable substance. We also highlight bottlenecks of the vitamin B6 biosynthetic pathways and propose strategies to circumvent these limitations.

Enzymatic transamination of pyridoxamine in tobacco plants

Vitamin B6 (VB6) comprises a group of pyridine compounds that are involved in a surprisingly high diversity of biochemical reactions. Humans and animals depend largely on plants for their VB6 nutrition. Many studies have focused on biosynthesis of VB6 and comparatively little is known about VB6 metabolic conversion in plants. Recently, we have found that an efficient conversion pathway between pyridoxal (PL) and pyridoxamine (PM) is present in tobacco, but the catalytic enzyme remains an unsolved mystery. In this study, enzymes catalyzing the transamination of PM were purified from tobacco leaves and characterized. Our results suggest that a specific PM-pyruvate aminotranferase dominates the reversible transamination of PM in tobacco, and also show that the apo form of glutamic-oxaloacetic aminotranferase from tobacco, but not the holoenzyme, is able to catalyze the analogous transamination reaction between PM and either oxaloacetate or α-ketoglutarate. PM-pyruvate aminotranferase is involved in a degradation pathway for VB6 compounds in bacteria. Therefore, our study raises questions about whether the degradation pathway of VB6 exists in plants.

Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti

Pyridoxine 4-oxidase (PNOX) from Mesorhizobium loti is a monomeric glucose-methanol-choline (GMC) oxidoreductase family enzyme, catalyzes FAD-dependent oxidation of pyridoxine (PN) into pyridoxal, and is the first enzyme in pathway I for the degradation of PN. The tertiary structures of PNOX with a C-terminal His6-tag and PNOX-pyridoxamine (PM) complex were determined at 2.2Å and at 2.1Å resolutions, respectively. The overall structure consisted of FAD-binding and substrate-binding domains. In the active site, His460, His462, and Pro504 were located on the re-face of the isoalloxazine ring of FAD. PM binds to the active site through several hydrogen bonds. The side chains of His462 and His460 are located at 2.7 and 3.1Å from the N4' atom of PM. The activities of His460Ala and His462Ala mutant PNOXs were very low, and 460Ala/His462Ala double mutant PNOX exhibited no activity. His462 may act as a general base for the abstraction of a proton from the 4'-hydroxyl of PN. His460 may play a role in the binding and positioning of PN. The C4' atom in PM is located at 3.2Å, and the hydride ion from the C4' atom may be transferred to the N5 atom of the isoalloxazine ring. The comparison of active site residues in GMC oxidoreductase shows that Pro504 in PNOX corresponds to Asn or His of the conserved His-Asn or His-His pair in other GMC oxidoreductases. The function of the novel proline residue was discussed.

All-enzymatic HPLC method for determination of individual and total contents of vitamin B(6) in foods

Background

There is a need for a reliable and accurate method for quantification of each of the seven individual vitamin B₆ compounds including pyridoxine-β-glucoside in foods.

Objective

To determine pyridoxal (PL), pyridoxamine (PM), pyridoxine (PN), pyridoxal 5′-phosphate (PLP), pyridoxamine 5′-phosphate (PMP), pyridoxine 5′-phosphate (PNP), and pyridoxine-β-glucoside (PNG) in foods.

Design

By specific enzymatic treatment, each of the seven vitamin B₆ compounds was all converted into 4-pyridoxolactone, which is a highly fluorescent compound. In total, seven separate, enzymatic steps were performed for each sample. Separation and quantification were performed with reversed-phase high performance liquid chromatography (HPLC) coupled with fluorescence detection. For each sample type the result was corrected for the recovery based on spiked samples. The method was applied for analyses of chicken liver, chicken white meat, egg yolk, egg white, dried anchovy, carrots, and garlic.

Results

The recovery varied from 14 to 114% in chicken liver, chicken white meat, egg yolk, egg white, dried anchovy, carrot, and garlic. Each food showed a characteristic distribution of the seven vitamin B₆ compounds. The PNG was only found in low amounts; that is, 17–29nmol vitamin B₆/g in the plant-derived foods, carrot and garlic. Only egg white showed a lower content, 3nmol/g. Overall the content in chicken liver, chicken white meat, and egg yolk had a total content of vitamin B₆ between 42 and 51nmol/g. Both PM and PMP were high in the chicken liver. In contrast, PL and PLP were high in the chicken white meat. The main vitamin B₆ in the egg yolk was PLP. The dried anchovy contained high amounts of PLP and PMP and a total content of 144nmol/g.

Conclusions

The enzymatic-based HPLC method was applied for the determination of seven vitamin B6 compounds in foods. Their distribution in the foods varied significantly.

Interconversions of different forms of vitamin B6 in tobacco plants

There are six different vitamin B(6) (VB(6)) forms, pyridoxal (PL), pyridoxamine (PM), pyridoxine (PN), pyridoxal 5'-phosphate (PLP), pyridoxamine 5'-phosphate (PMP), and pyridoxine 5'-phosphate (PNP), of which PLP is the active form. Although plants are a major source of VB(6) in the human diet, and VB(6) plays an important role in plants, the mechanisms underlying the interconversions of different VB(6) forms are not well understood. In this study, in vitro tobacco plants were grown on Murashige and Skoog (MS) basal media supplemented with 100mg/L of PM, PL or PN and the abundance of the different B(6) vitamers in leaf tissue was quantified by high performance liquid chromatography (HPLC). The total amount of VB(6) was about 3.9 μg/g fresh weight of which PL, PM, PN, PLP and PMP accounted for 23%, 14%, 37%, 20% and 6%, respectively. Tobacco plants contained a trace amount of PNP. Supplementation of the culture medium with any of the non-phosphorylated vitamers resulted in an increase in total VB(6) by about 10-fold, but had very little impact on the concentrations of the endogenous phosphorylated vitamers. Administration of either PM or PN increased their endogenous levels more than the levels of any other endogenous B(6) vitamers. PL supplementation increased the levels of plant PN and PM significantly, but not that of PL, suggesting that efficient conversion pathways from PL to PN and PM are present in tobacco. Additionally, maintenance of a stable level of PLP in the plant is not well-correlated to changes in levels of non-phosphorylated forms.

Characterization of enzymes involved in the interconversions of different forms of vitamin B(6) in tobacco leaves

There are six different vitamin B(6) (VB(6)) forms, pyridoxal (PL), pyridoxamine (PM), pyridoxine (PN), pyridoxal 5'-phosphate (PLP), pyridoxamine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP). PLP is a coenzyme required by more than 100 cellular enzymes. In spite of the importance of this vitamin, the understanding of VB(6) metabolic conversion in plants is limited. In this study, we developed a sensitive and reliable method to assay VB(6)-metabolizing enzyme activities by monitoring their products visually using high-performance liquid chromatography. With this method, the reactions catalyzed by PL/PM/PN kinase, PMP/PNP oxidase, PM-pyruvate aminotransferase, PL reductase and PLP phosphatase were all nicely detected using crude protein extracts of tobacco leaves. Under optimal in vitro conditions, specific activities of those enzymes were 0.15 ± 0.03, 0.10 ± 0.03, 0.08 ± 0.02, 0.64 ± 0.13 and 23.08 ± 1.98 nmol product/min/mg protein, respectively. This is the first report on the conversion between PM and PL catalyzed by PM-pyruvate aminotransferase in plants. Furthermore, the PL reductase activity was found to be heat inducible. Our study sheds light on the VB(6) metabolism taking place in plants.

Pyridoxal phosphate: biosynthesis and catabolism

Vitamin B(6) is an essential cofactor that participates in a large number of biochemical reactions. Pyridoxal phosphate is biosynthesized de novo by two different pathways (the DXP dependent pathway and the R5P pathway) and can also be salvaged from the environment. It is one of the few cofactors whose catabolic pathway has been comprehensively characterized. It is also known to function as a singlet oxygen scavenger and has protective effects against oxidative stress in fungi. Enzymes utilizing vitamin B(6) are important targets for therapeutic agents. This review provides a concise overview of the mechanistic enzymology of vitamin B(6) biosynthesis and catabolism. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.

Development of simultaneous enzymatic assay method for all six individual vitamin B6 forms and pyridoxine-beta-glucoside

A method for determining all of the six natural vitamin B(6) compounds and pyridoxine-beta-glucoside in urine from humans consuming their usual diet was developed. These compounds were specifically converted with 5 enzymes into a high fluorescent 4-pyridoxolactone which was supersensitively determined by an isocratic HPLC. All of the compounds in urine from humans consuming their usual diets were for the first time determined together. The preparation procedure for urine samples was easy without HCl-hydrolysis, and the enzyme reactions took only 2 or 3 h. It required only 5 microL of the urine sample for analysis of one of the compounds. Urine samples from five young Japanese males consuming their usual diet contained pyridoxal, pyridoxamine, and pyridoxine-beta-glucoside but not pyridoxine or phosphoester forms. The contents of 4-pyridoxic acid and pyridoxal correlate well with a correlation coefficient of 0.98. On the other hand, the content of pyridoxamine did not correlate with that of 4-pyridoxic acid.

Gene identification and characterization of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD+-dependent dismutase

A chromosomal gene, mlr6793, in Mesorhizobium loti was identified as the gene encoding 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) dehydrogenase (dismutase) involved in the degradation pathway for pyridoxine (vitamin B(6)). The homogenously purified recombinant enzyme has a molecular mass of 59.1 kDa and is a homodimeric protein. FHMPC dehydrogenase catalyses practically irreversible oxidation (k(cat) = 204 s(-1)) of FHMPC (K(m) = 48.2 microM) by NAD(+) (K(m) = 34.3 microM) to 3-hydroxy-2-methyl-pyridine 4, 5-dicarboxylic acid (HMPDC), and practically irreversible reduction (k(cat) = 217 s(-1)) of FHMPC (K(m) = 24.9 microM) by NADH (K(m) = 12.4 microM) to 4-pyridoxic acid. When the enzyme reaction was started with the combination of FHMPC and NAD(+) or that of FHMPC and NADH, HMPDC and 4-pyridoxic acid were produced in an almost equimolar ratio throughout the reaction. FHMPC dehydrogenase belongs to the 3-hydroxyacyl-CoA dehydrogenase family with 31% identity with the human enzyme: it has probable catalytic diad residues, i.e. His137 and Glu149. The H137L mutant enzyme showed no measurable activity. The E149Q one was stable in contrast to the corresponding human 3-hydroxyacyl-CoA dehydrogenase mutant, and showed unique pH optima depending on the co-substrates used for the reaction.

Gene identification and characterization of the pyridoxine degradative enzyme alpha-(N-acetylaminomethylene)succinic acid amidohydrolase from Mesorhizobium loti MAFF303099

We have found for the first time that a chromosomal gene, mlr6787, in Mesorhizobium loti encodes the pyridoxine degradative enzyme alpha-(N-acetylaminomethylene)succinic acid (AAMS) amidohydrolase. The recombinant enzyme expressed in Escherichia coli cells was homogeneously purified and characterized. The enzyme consisted of two subunits each with a molecular mass of 34,000+/-1,000 Da, and exhibited Km and kcat values of 53.7+/-6 microM and 307.3+/-12 min(-1), respectively. The enzyme required no cofactor or metal ion. The primary structure of AAMS amidohydrolase was elucidated for the first time here. The primary structure of the enzyme protein showed no significant identity to those of known hydrolase proteins and low homology to those of fluoroacetate dehalogenase (PDB code, 1Y37), haloalkane dehalogenase (1K5P), and aryl esterase (1VA4).

Molecular cloning, identification and characterization of 2-methyl-3-hydroxypyridine-5-carboxylic-acid-dioxygenase-coding gene from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti

The gene (mlr6788) of a nitrogen-fixing symbiotic bacterium Mesorhizobium loti MAFF303099 has been identified as a gene coding for 2-methyl-3-hydroxypyridine-5-carboxylic acid dioxygenase (MHPCO), the seventh enzyme in degradation pathway I for pyridoxine, a free form of vitamin B(6). The gene was cloned and overexpressed in Escherichia coli cells co-transformed with chaperonin genes. The homogeneous recombinant enzyme showed similar enzymatic properties to the enzyme from Pseudomonas sp. MA-1. MHPCO was essential for the assimilation of pyridoxine in M. loti, but not for its growth in a nutrient-rich medium. From the infection experiment of a symbiotic plant Lotus japonicus with an M. loti mlr6788 gene disruptant, MHPCO was demonstrated to be dispensable for at least nodule formation on roots of seedlings in symbiosis.

Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti

We have found for the first time that a chromosomal gene, mlr6807, in Mesorhizobium loti encodes a new tetrameric pyridoxal 4-dehydrogenase (PLDH). The recombinant enzyme expressed in Escherichia coli cells was homogenously purified and characterized. The enzyme consisted of four subunits each with a molecular weight of 26,000+/-1000, and exhibited Km and kcat values of 91+/-2 microM and 149+/-1s(-1), respectively. PLDH used NAD+ as a cosubstrate, showed no activity toward sugars, and belonged to a short-chain dehydrogenase/reductase family. The mlr6807 gene-disrupted M. loti cells could grow in a nutrient-rich TY medium but not in a synthetic one containing pyridoxine or pyridoxamine as the sole carbon and nitrogen source. Thus, it was found that PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway in M. loti.