Analysis of the Vitamin B6 Biosynthesis Pathway in the Human Malaria Parasite Plasmodium falciparum

Wrenger, Carsten; Eschbach, Marie‐Luise; Müller, Ingrid; Warnecke, Dirk; Walter, Rolf D.

doi:10.1074/jbc.m412475200

Cited by 91 publications

(70 citation statements)

References 50 publications

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“…The isolation of active protein was confirmed by the ability of YaaE to catalyze the hydrolysis of glutamine, an activity that is dependent on YaaD, its partner protein. (24). However, there is typically a large variation in the amount of activity observed in the glutaminase family of proteins, depending on whether the acceptor domain and its substrates are present or not.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, 15 N-labeling studies in yeast had indicated that the nitrogen atom of pyridoxine is derived from the amide moiety of glutamine (9,10), whereas in the E. coli pathway it is derived from glutamate (10,21). Indeed, glutaminase activity has since been demonstrated for the PDX2 proteins of B. subtilis, Saccharomyces cerevisiae, and Plasmodium falciparum (22)(23)(24), designated YaaE (PdxT), SNO1, and PDX2, respectively. However, glutaminase activity was only observed in the presence of PDX1, which was shown to co-purify with PDX2, forming a hetero-oligomeric complex as has been observed for other glutamine amidotransferases (22,23).…”

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confidence: 99%

“…In general, glutamine amidotransferases consist of two domains, a glutaminase domain, which hydrolyzes glutamine to glutamate and ammonia, and a synthase domain that accepts and utilizes the ammonia from the glutaminase domain (19). It was, therefore, postulated that PDX1 is likely to be the synthase subunit of the glutamine amidotransferase hetero-oligomeric complex (22)(23)(24), but the nature of the substrates in the synthase reaction remained unknown. Nonetheless, extensive labeling studies in yeast had established that the origin of the C5-chain C-2Ј,2,3,4,4Ј of pyridoxamine is derived from an intact glucose-derived pentulose and/or pentose intermediate rather than deoxy-D-xylulose s-phosphate as in E. coli (25), and more recently a genetic study in yeast indicated that the five-carbon sugar might be ribulose 5-phosphate (26), but the identity of the remaining triose sugar remained elusive (12).…”

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confidence: 99%

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On the Two Components of Pyridoxal 5′-Phosphate Synthase from Bacillus subtilis

Raschle

Amrhein

Fitzpatrick

2005

Journal of Biological Chemistry

118

163

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Vitamin B6 is an essential nutrient in the human diet. It can act as a co-enzyme for numerous metabolic enzymes and has recently been shown to be a potent antioxidant. Plants and microorganisms have the ability to make the compound. Yet, studies of vitamin B6 biosynthesis have been mainly restricted to Escherichia coli, where the vitamin is synthesized from 1-deoxy-D-xylulose 5-phosphate and 4-phosphohydroxy-L-threonine. Recently, a novel pathway for its synthesis has been discovered, involving two genes (PDX1 and PDX2) neither of which is homologous to any of those participating in the E. coli pathway. In Bacillus subtilis, YaaD and YaaE represent the PDX1 and PDX2 homolog, respectively. The two proteins form a complex that functions as a glutamine amidotransferase, with YaaE as the glutaminase domain and YaaD as the acceptor and pyridoxal 5-phosphate (PLP) synthesis domain. In this report we corroborate a recent report on the identification of the substrates of YaaD and provide unequivocal proof of the identity of the reaction product. We show that both the glutaminase and synthase reactions are dependent on the respective protein partner. The synthase reaction can also utilize an external ammonium source but, in contrast to other glutamine amidotransferases, is dependent on YaaE under certain conditions. Furthermore, we report on the detailed characterization of the inhibition of the glutaminase domain, and thus PLP synthesis, by the glutamine analog acivicin. Employing pull-out assays and native-PAGE, we provide evidence for the dissociation of the bi-enzyme complex under these conditions. The results are discussed in light of the nature of the interaction of the two components of the enzyme complex.In humans vitamin B6 is required for the maintenance of health. From a biochemical point of view the vitamin is well recognized in its active form as pyridoxal 5Ј-phosphate (PLP), 2 one of nature's most versatile cofactors and required for many diverse enzymes ranging from amino acid metabolism to the biosynthesis of antibiotic compounds. Furthermore, very recently, the B6 vitamers have been shown to be potent antioxidants equivalent to vitamins C and E, effectively quenching the reactive oxygen species singlet oxygen and superoxide anion in vitro (1, 2). Vitamin B6 is synthesized in bacteria, fungi, and plants; yet, despite its essential role, its biosynthesis has been studied at the enzymatic level essentially only in the Gram-negative bacterium Escherichia coli (3-7) where it is derived from D-erythrose-4-phosphate, deoxy-Dxylulose 5-phosphate, and glutamate (5, 8 -10) (Scheme 1). The biosynthesis of the vitamin has recently come back into scrutiny, because it has become clear from studies in fungi that a pathway different from that in E. coli exists (1,(11)(12)(13)(14).Two of the key genes involved in this novel pathway have been identified (PDX1 and PDX2) (1,(15)(16)(17), neither of which show similarity to any of the E. coli genes (1, 15, 16). At the outset, amino acid sequence alignment studies indicated t...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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On the Two Components of Pyridoxal 5′-Phosphate Synthase from Bacillus subtilis

Raschle

Amrhein

Fitzpatrick

2005

Journal of Biological Chemistry

118

163

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“…PDX1 and PDX2 have been predicted to function as a glutamine amidotransferase with PDX2 as the glutaminase domain and PDX1 as the acceptor͞synthase domain. Indeed, glutaminase activity has been demonstrated for PDX2 from a number of organisms (16)(17)(18). More recently, Burns et al (19) and our own independent studies (51) have been able to reconstitute vitamin B6 formation from intermediates of glycolysis and the pentose phosphate pathway by using the PDX1 and PDX2 homologs from the Gram-positive bacterium Bacillus subtilis.…”

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confidence: 93%

Vitamin B6 biosynthesis in higher plants

Tambasco-Studart

Titiz²,

Raschle³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

212

260

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Vitamin B6 is an essential metabolite in all organisms. It can act as a coenzyme for numerous metabolic enzymes and has recently been shown to be a potent antioxidant. Plants and microorganisms have a de novo biosynthetic pathway for vitamin B6, but animals must obtain it from dietary sources. In Escherichia coli, it is known that the vitamin is derived from deoxyxylulose 5-phosphate (an intermediate in the nonmevalonate pathway of isoprenoid biosynthesis) and 4-phosphohydroxy-L-threonine. It has been assumed that vitamin B6 is synthesized in the same way in plants, but this hypothesis has never been experimentally proven. Here, we show that, in plants, synthesis of the vitamin takes an entirely different route, which does not involve deoxyxylulose 5-phosphate but instead utilizes intermediates from the pentose phosphate pathway, i.e., ribose 5-phosphate or ribulose 5-phosphate, and from glycolysis, i.e., dihydroxyacetone phosphate or glyceraldehyde 3-phosphate. The revelation is based on the recent discovery that, in bacteria and fungi, a novel pathway is in place that involves two genes (PDX1 and PDX2), neither of which is homologous to any of those involved in the previously doctrined E. coli pathway. We demonstrate that Arabidopsis thaliana has two functional homologs of PDX1 and a single homolog of PDX2. Furthermore, and contrary to what was inferred previously, we show that the pathway appears to be cytosolic and is not localized to the plastid. Last, we report that the single PDX2 homolog is essential for plant viability.Arabidopsis ͉ isoprenoid ͉ pyridoxine ͉ deoxyxylulose 5-phosphate V itamin B6 is well renowned in the medical field for being involved in more bodily functions than any other single nutrient. The vitamin exists in various forms, i.e., pyridoxal, pyridoxine, pyridoxamine, and their phosphorylated derivatives. As pyridoxal 5Ј-phosphate, it is an essential cofactor for numerous metabolic enzymes including amino acid metabolism and antibiotic biosynthesis. Most interestingly, it has recently been found that the vitamin is a potent antioxidant with a particular ability to quench reactive oxygen species such as superoxide and singlet oxygen (1, 2). The de novo biosynthesis of vitamin B6 takes place in microorganisms and plants, but this ability has been lost in animals, making it essential in the human diet.Despite the vitamin's obvious physiological and pharmaceutical importance, its biosynthesis has predominantly been studied in the Gram-negative bacterium, Escherichia coli, where it is derived from deoxyxylulose 5-phosphate (DXP, an intermediate in the nonmevalonate pathway of isoprenoid biosynthesis) and 4-phosphohydroxy-L-threonine (refs. 3-7 and Scheme 1). Astonishingly, although plants are a major source of vitamin B6 in the human diet, our understanding of the pathway therein is very limited and has been assumed to be derived the same way as in E. coli. There is one preliminary study that reports on its biosynthesis in spinach (8), whereas other, more in-depth studies have addressed the...

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“…The term "vitamin B6" collectively refers to the vitamers pyridoxal, pyridoxine, and pyridoxamine, and their respective phosphate esters. The metabolically active form is pyridoxal 5Ј-phosphate (PLP), 6 an essential co-enzyme in numerous pathways such as amino acid metabolism and the biosynthesis of antibiotic compounds. In contrast to mammals, which have to take up vitamin B6 from their diet, bacteria, fungi, plants, and the protozoan P. falciparum have the ability to synthesize the vitamin de novo.…”

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Vitamin B6 Biosynthesis by the Malaria Parasite Plasmodium falciparum

Gengenbacher

Fitzpatrick

Raschle

et al. 2006

Journal of Biological Chemistry

116

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Vitamin B6 is one of nature's most versatile cofactors. Most organisms synthesize vitamin B6 via a recently discovered pathway employing the proteins Pdx1 and Pdx2. Here we present an in-depth characterization of the respective orthologs from the malaria parasite, Plasmodium falciparum. Expression profiling of Pdx1 and -2 shows that blood-stage parasites indeed possess a functional vitamin B6 de novo biosynthesis. Recombinant Pdx1 and Pdx2 form a complex that functions as a glutamine amidotransferase with Pdx2 as the glutaminase and Pdx1 as pyridoxal-5-phosphate synthase domain. Complex formation is required for catalytic activity of either domain. Pdx1 forms a chimeric bi-enzyme with the bacterial YaaE, a Pdx2 ortholog, both in vivo and in vitro, although this chimera does not attain full catalytic activity, emphasizing that species-specific structural features govern the interaction between the protein partners of the PLP synthase complexes in different organisms. To gain insight into the activation mechanism of the parasite bi-enzyme complex, the three-dimensional structure of Pdx2 was determined at 1.62 Å . The obstruction of the oxyanion hole indicates that Pdx2 is in a resting state and that activation occurs upon Pdx1-Pdx2 complex formation.Plasmodium falciparum is the causative agent of severe malaria. Each year up to two million human deaths and enormous economic losses are attributed to this parasite. Drug resistance in P. falciparum has been aggravating the problem in many parts of the world during the last two decades, which considering the lack of a protective vaccine, is the major obstacle to combat the disease. Hence, new antimalarials are urgently needed. Requirements for nutrients and vitamins have previously been discussed as possible novel targets (1). Indeed the P. falciparum genome contains genes that encode enzymes necessary for the syntheses of the vitamin precursor chorismate (2-4), vitamin B6 (5, 6), and the vitaminlike cofactor lipoic acid (7).Vitamin B6 is renowned in the medical field as being involved in more bodily functions than any other single nutrient. It is required for the maintenance of physical as well as mental health. The term "vitamin B6" collectively refers to the vitamers pyridoxal, pyridoxine, and pyridoxamine, and their respective phosphate esters. The metabolically active form is pyridoxal 5Ј-phosphate (PLP), 6 an essential co-enzyme in numerous pathways such as amino acid metabolism and the biosynthesis of antibiotic compounds. In contrast to mammals, which have to take up vitamin B6 from their diet, bacteria, fungi, plants, and the protozoan P. falciparum have the ability to synthesize the vitamin de novo.Analyses of a number of available genomes has demonstrated that most organisms, including all archaea, fungi, plants, and protozoa and most eubacteria use a class I glutamine amidotransferase (GATase) composed of two domains, a glutaminase and its associated acceptor/ synthase domain to generate vitamin B6 (8 -13). Structural knowledge on class I GATases in genera...

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Analysis of the Vitamin B6 Biosynthesis Pathway in the Human Malaria Parasite Plasmodium falciparum

Cited by 91 publications

References 50 publications

On the Two Components of Pyridoxal 5′-Phosphate Synthase from Bacillus subtilis

On the Two Components of Pyridoxal 5′-Phosphate Synthase from Bacillus subtilis

Vitamin B6 biosynthesis in higher plants

Vitamin B6 Biosynthesis by the Malaria Parasite Plasmodium falciparum

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