[논문]Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes

Tanaka, Tsuyoshi; Tateno, Yoshio; Gojobori, Takashi

doi:10.1093/molbev/msi011

Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes 원문보기

Molecular biology and evolution, v.22 no.2, 2005년, pp.243 - 250

Tanaka, Tsuyoshi , Tateno, Yoshio , Gojobori, Takashi

Abstract ▼ AI-Helper

Vitamin B(6) (VB6) functions as a cofactor of many diverse enzymes in amino acid metabolism. Three metabolic pathways for pyridoxal 5'-phosphate (PLP; the active form of VB6) are known: the de novo pathway, the salvage pathway, and the fungal type pathway. Most unicellular organisms and plants biosynthesize VB6 using one or two of these three biosynthetic pathways. However, animals such as insects and mammals do not possess any of the pathways and, thus, need to intake VB6 in their diet to survive. It is conceivable that breakdowns of these pathways occurred in the evolutionary lineages of insects and mammals, and one of the major reasons for this would be the loss of pertinent genes. We studied the evolution of VB6 biosynthesis from the view of the gain and loss of 10 pertinent genes in 122 species whose genome sequences were completely determined. The results revealed that each gene in the pathways was lost more than once in the entire evolutionary lineages of the 122 species. We also found the following three points regarding the evolution of PLP biosynthesis: (1) the breakdown of the PLP biosynthetic pathways occurred independently at least three times in animal lineages, (2) the de novo pathway was formed by the generation of pdxB in gamma-proteobacteria, and (3) the order of the gene loss in VB6 metabolism was conserved among different evolutionary lineages. These results suggest that the evolution of VB6 metabolism was subject to gains and frequent losses of related genes in the 122 species examined. This dynamic nature of the evolutionary changes must have been responsible for the breakdowns of the pathways, resulting in profound differentiation of heterotrophy among the species.

참고문헌 (38)

10.1016/S0022-2836(05)80360-2 Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol.215:403-410.

상세보기
10.1126/science.290.5493.972 Baldauf, S. L., A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of Eukaryotas based on combined protein data. Science290:972-927.

상세보기
10.1093/genetics/157.3.1067 Bean, L. E., W. H. Dvorachek Jr, E. L. Braun, A. Errett, G. S. Saenz, M. D. Giles, M. Werner-Washburne, M. A. Nelson, and D. O. Natvig. 2001. Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: correlation of pyridoxine-requiring phenotypes with mutations in two structural genes. Genetics157:1067-1075.

상세보기
10.1562/0031-8655(2000)071<0129:SIPVBP>2.0.CO;2 Bilski, P., M. Y. Li, M. Ehrenshaft, M. E. Daub, and C. F. Chignell. 2000. VB6 (pyridoxine) and its derivatives are efficient singlet oxygen quenchers and potential fungal antioxidants. Photochem. Photobiol.71:129-134.

상세보기
Bono, H., S. Goto, W. Fujibuchi, H. Ogata, and M. Kanehisa. 1998. Systematic prediction of orthologous units of genes in the complete genomes. Genome Inform. Ser. Workshop Genome Inform.9:32-40.
10.1073/pnas.96.16.9374 Ehrenshaft, M., P. Bilski, M. Y. Li, C. F. Chignell, and M. E. Daub. 1999. A highly conserved sequence is a novel gene involved in de novo VB6 biosynthesis. Proc. Natl. Acad. Sci. USA96:9374-938.

상세보기
10.1128/JB.183.11.3383-3390.2001 Ehrenshaft, M., and M. E. Daub. 2001. Isolation of PDX2, a second novel gene in the pyridoxine biosynthesis pathway of eukaryotes, archaebacteria, and a subset of eubacteria. J. Bacteriol.183:3383-3390.

상세보기
10.1007/BF00408308 Grogan, D. W. 1988. Temperature-sensitive murein synthesis in an Escherichia coli pdx mutant and the role of alanine racemase. Arch. Microbiol.150:363-367.

상세보기
Helmreich, E. J. 1992. How pyridoxal 5′-phosphate could function in glycogen phosphorylase catalysis. Biofactors3:159-172.
10.1073/pnas.31.6.153 Horowitz, N. H. 1945. On the evolution of biochemical synthesis. Proc. Natl. Acad. Sci. USA31:152-157.

상세보기
10.1016/S0966-842X(99)01539-5 Huynen, M. A., T. Dandekar, and P. Bork. 1999. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol.7:281-291.

상세보기
10.1146/annurev.mi.30.100176.002205 Jensen, R. A. 1976. Enzyme recruitment on evolution of new function. Annu. Rev. Microbiol.30:409-425.

상세보기
10.1006/jmbi.1999.2997 Kack, H., J. Sandmark, K. Gibson, G. Schneider, and Y. Lindqvist. 1999. Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5′-phosphate-dependent enzymes. J. Mol. Biol.291:857-876.

상세보기
10.1093/nar/30.1.42 Kanehisa, M., S. Goto, S. Kawashima, and A. Nakaya. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res.30:42-46.

상세보기
10.1093/nar/30.1.56 Karp, P. D., M. Riley, M. Saier, I. T. Paulsen, J. Collado-Vides, S. M. Paley, A. Pellegrini-Toole, C. Bonavides, and S. Gama-Castro. 2002. The EcoCyc database. Nucleic Acids Res.30:56-58.

상세보기
10.1128/jb.172.11.6518-6528.1990 Lam, H. M., and M. E. Winkler. 1990. Metabolic relationships between pyridoxine (VB6) and serine biosynthesis in Escherichia coli K-12. J. Bacteriol.172:6518-6528.

상세보기
10.1128/jb.178.8.2445-2449.1996 Man, T. K., G. Zhao, and M. E. Winkler. 1996. Isolation of a pdxJ point mutation that bypasses the requirement for the PdxH oxidase in pyridoxal 5′-phosphate coenzyme biosynthesis in Escherichia coli K-12. J. Bacteriol.178:2445-2449.

상세보기
10.1093/ajcn/72.2.598S Manore, M. M. 2000. Effect of physical activity on thiamine, riboflavin, and VB6 requirements. Am. J. Clin. Nutr.72:598S-606S.

상세보기
10.1016/S0083-6729(01)61006-9 Meganathan, R. 2001. Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms. Vitam. Horm.61:173-218.
10.1074/jbc.272.36.22417 Mihara, H., T. Kurihara, T. Yoshimura, K. Soda, and N. Esaki. 1997. Cysteine sulfinate desulfinase, a NIFS-like protein of Escherichia coli with selenocysteine lyase and cysteine desulfurase activities: gene cloning, purification, and characterization of a novel pyridoxal enzyme. J. Biol. Chem.272:22417-22424.

상세보기
Mittenhuber, G. 2001. Phylogenetic analyses and comparative genomics of VB6 (pyridoxine) and pyridoxal phosphate biosynthesis pathways. J. Mol. Microbiol. Biotechnol.3:1-20.
10.1038/ng1381 Nakamura, Y., T. Itoh, H. Matsuda, and T. Gojobori. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet.36:760-766.

상세보기
10.1038/80235 Nelson, K. E., I. T. Paulsen, J. F. Heidelberg, and C. M. Fraser. 2000. Status of genome projects for nonpathogenic bacteria and archaea. Nat. Biotechnol.18:1049-1054.

상세보기
10.1074/jbc.274.33.23565 Osmani, A. H., G. S. May, and S. A. Osmani. 1999. The extremely conserved pyroA gene of Aspergillus nidulans is required for pyridoxine synthesis and is required indirectly for resistance to photosensitizers. J. Biol. Chem.274:23565-23569.

상세보기
10.1016/0022-2836(91)90587-V Rottmann, W. H., G. F. Peter, P. W. Oeller, J. A. Keller, N. F. Shen, B. P. Nagy, L. P. Taylor, A. D. Campbell, and A. Theologis. 1991. 1-aminocyclopropane-1-carboxylate synthase in tomato is encoded by a multigene family whose transcription is induced during fruit and floral senescence. J. Mol. Biol.222:937-961.

상세보기
10.1016/S0968-0004(03)00114-2 Schmidt, S., S. Sunyaev, P. Bork, and T. Dandekar. 2003. Metabolites: a helping hand for pathway evolution?. Trends Biochem. Sci.28:336-341.

상세보기
10.1016/S0167-4781(01)00246-9 Seack, J., S. Perovic, V. Gamulin, H. C. Schroder, P. Beutelmann, I. M. Muller, and W. E. Muller. 2001. Identification of highly conserved genes: SNZ and SNO in the marine sponge Suberites domuncula: their gene structure and promoter activity in mammalian cells(1). Biochim. Biophys. Acta.1520:21-34.

상세보기
10.1128/jb.179.16.5218-5221.1997 Seta, F. D., S. Boschi-Muller, M. L. Vignais, and G. Branlant. 1997. Characterization of Escherichia coli strains with gapA and gapB genes deleted. J. Bacteriol.179:5218-5221.

상세보기
10.1038/35024074 Shigenobu, S., H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature407:81-86.

상세보기
10.1016/S0083-6729(01)61008-2 Smirnoff, N. 2001. L-ascorbic acid biosynthesis. Vitam. Horm.61:241-266.
10.1016/S0960-9822(02)00478-5 Tatusov, R. L., A. R. Mushegian, P. Bork, N. P. Brown, W. S. Hayes, M. Borodovsky, K. E. Rudd, and E. V. Koonin. 1996. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr. Biol.6:279-291.

상세보기
10.1093/nar/22.22.4673 Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res.11:4673-4680.
10.1021/bi00823a005 White, R. S., and W. B. Dempsey. 1970. Purification and properties of VB6 kinase from Escherichia coli B. Biochemistry9:4057-4064.

상세보기
10.1073/pnas.87.12.4576 Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA87:4576-4579.

상세보기
10.1111/j.1574-6968.1996.tb08368.x Yang, Y., G. Zhao, and M. E. Winkler. 1996. Identification of the pdxK gene that encodes pyridoxine (VB6) kinase in Escherichia coli K-12. FEMS Microbiol. Lett.141:89-95.

상세보기
10.1128/JB.180.16.4294-4299.1998 Yang, Y., G. Zhao, T. K. Man, and M. E. Winkler. 1998a. Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5′-phosphate coenzyme biosynthesis in Escherichia coli K-12. J. Bacteriol.180:4294-4299.

상세보기
Yang, Y., H. C. Tsui, T. K. Man, and M. E. Winkler. 1998b. Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5′-phosphate biosynthesis in Escherichia coli K-12. J. Bacteriol.180:1814-1821.
10.1128/jb.177.10.2804-2812.1995 Zhao, G., A. J. Pease, N. Bharani, and M. E. Winkler. 1995. Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5′-phosphate biosynthesis. J. Bacteriol.177:2804-2812.

상세보기

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Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes 원문보기

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