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Phylogenetic Analyses and Comparative Genomics of Vitamin B6 (Pyridoxine) and Pyridoxal Phosphate Biosynthesis Pathways

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Phylogenetic Analyses and Comparative Genomics of Vitamin B6 (Pyridoxine) and Pyridoxal Phosphate Biosynthesis Pathways J. Mol. Microbiol. Biotechnol. (2001) 3(1): 1-20. Different Pyridoxine and Pyridoxal Phosphate BiosynthesisJMMB Pathways Review 1 Phylogenetic Analyses and Comparative Genomics of Vitamin B6 (Pyridoxine) and Pyridoxal Phosphate Biosynthesis Pathways Gerhard Mittenhuber* bacterial lineage. This proposal might help to explain why the PdxA/PdxJ pathway is largely restricted to this Institut für Mikrobiologie und Molekularbiologie, Ernst- subdivision. Moritz-Arndt-Universität, F.-L. Jahnstr. 15, D-17487 Greifswald, Germany Introduction Pyridoxal 5'-phosphate (PLP), the active form of vitamin Abstract B6, is an essential cofactor of many enzymes involved in amino acid metabolism in all cells (for reviews see Dolphin Vitamin B6 in its active form pyridoxal phosphate is et al., 1986; Dakshinamurti, 1990). The most common an essential coenzyme of many diverse enzymes. reactions involve (1) transaminases catalyzing the Biochemistry, enzymology and genetics of de novo conversion of α-ketoacids to amino acids, and (2) amino vitamin B6 biosynthesis have been primarily acid racemases producing D-amino acids originating from investigated in Escherichia coli. Database searches L-amino acids (Grogan, 1988). But PLP is also a coenzyme revealed that the key enzymes involved in ring closure of (3) sulfinate desulfinase catalyzing the removal of of the aromatic pyridoxin ring (PdxA; PdxJ) are present elemental sulfur and selenium atoms from L-cysteine, L- mainly in genomes of bacteria constituting the γ cystine, L-selenocysteine, and L-selenocystine to produce subdivision of proteobacteria. The distribution of DXS, L-alanine (Mihara et al., 1997), (4) of glycogen a transketolase-like enzyme involved in vitamin B6 phosphorylases (Helmreich, 1992), (5) of biosynthesis as well as in thiamine and isoprenoid diaminopelargonic acid synthase, an enzyme involved in biosynthesis and the distribution of vitamin B6 biotin synthesis (Kack et al., 1999) and (6) of 1- modifying enzymes (PdxH: oxidase; PdxK: kinase) was aminocyclopropane-1-carboxylate synthase (Rottmann et also analyzed. These enzymes are also present in the al., 1991) synthesizing 1-aminocyclopropane-1-carboxylic genomes of animals. Two recent papers (Ehrenshaft acid (ACC) - the precursor of the plant hormone ethylene - et al., 1999, Proc. Natl. Acad. Sci. USA. 96 : 9374-9378; from S-adenosylmethionine. Despite these vast differences Osmani et al., 1999, J. Biol. Chem. 274 : 23565-23569) in the nature of the reactions catalyzed by PLP-dependent show the involvement of an extremely conserved enzymes, their three-dimensional structures share common protein (a member of the UPF0019 or SNZ family) found structural elements (Capitani et al., 1999, Denessiouk et in all three domains of life (bacteria, archaea, eukarya) al., 1999, Kack et al., 1999, Schneider et al., 2000). in an alternative vitamin B6 biosynthesis pathway. The biochemistry of de novo PLP biosynthesis has Members of this family were previously identified as a been studied in the gramnegative model organism stationary phase inducible protein in yeast, as an Escherichia coli (Hill and Spenser, 1996). Also, molecular ethylene responsible protein in plants and in a marine cloning and characterization of genes coding for enzymes sponge, as a singlet oxygen resistance protein in involved in PLP biosynthesis was performed using this Cercospora nicotianae and as a cumene organism, mainly by Malcolm E. Winkler and coworkers: hydroperoxide and H2O2 inducible protein in Bacillus The PLP precursor pyridoxine 5'-phosphate (PNP) is subtilis. In yeast, the SNZ protein interacts with another synthesized by the PdxA and PdxJ enzymes using 4- protein called SNO which also represents a member phosphohydroxy-L-threonine (4PHT; synonym: 3- of a highly conserved protein family (called UPF0030 hydroxyhomoserine) and 1-deoxy-D-xylulose 5-phosphate or SNO family). Phylogenetic trees for the DXS, PdxA, (DXP) as substrates (Lam et al., 1992; Zhao and Winkler, PdxJ, PdxH, PdxK, SNZ and SNO protein families are 1996; Cane et al., 1998; Laber et al, 1999). PNP is oxidized presented and possible implications of the two to the active coenzyme PLP by the action of PdxH oxidase, different vitamin B6 biosynthesis pathways in cellular a flavoprotein (Lam and Winkler, 1992; Zhao and Winkler, metabolism are discussed. A radically different view 1995; Notheis et al., 1995). of bacterial evolution (Gupta, 2000, Crit. Rev. Microbiol. The two substrates DXP and 4PHT are supplied by 26: 111-131) which proposes a linear rather than a two independent pathways (Figure 1), which are both linked treelike evolutionary relationship between procaryotic to carbohydrate metabolism, i.e. glycolysis and the pentose species indicates that the γ subdivision of phosphate cyle: DXP, which is also a precursor in proteobacteria represents the most recently evolved isoprenoid and thiamine (vitamin B1) biosynthesis (Begley et al., 1999) is synthesized by the transketolase-like Received August 2, 2000; accepted September 4, 2000. *For correspondence. Email [email protected] enzyme DXP-synthase (DXS) (Sprenger et al., 1997; Lois greifswald.de; Tel. +49-3834-864218; Fax. +49-3834-864202. et al., 1998) using pyruvate and D-glyceraldehyde-3- © 2001 Horizon Scientific Press Further Reading Caister Academic Press is a leading academic publisher of advanced texts in microbiology, molecular biology and medical research. 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The key enzymes PdxA and PdxJ catalyze synthesis of the pyridine ring. The precursors 4PHT and DXP can be readily produced from intermediates of the pentose phosphate cycle and of glycolysis, respectively. Table 1. A comparison of the genes encoding pyridoxal 5'-phosphate biosynthesis enzymes of E. coli and orthologous open reading frames found in the B. subtilis genome. E. coli genes Enzymatic function of gene product References Similarities Predicted enzymatic function of gene product Expectation value coding for in B. subtilis enzymes involved in pyridoxine biosynthesis gapA Glyceraldehyde 3-P dehydrogenase
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