Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: A phylogenetic analysis of archaeal genomes

Archaea

Volumn 1, Issue 5, 2005, Pages 347-352

  Soderberg, Tim ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Aromatic amino acid biosynthesis; Chorismate; Genomic analysis; Nucleotide biosynthesis; Pentose phosphate pathway; Ribulose 5 phosphate; Transketolase

Indexed keywords

ARCHAEA; HALOBACTERIUM; HALOBACTERIUM SP.; HALOBACTERIUM SP. NRC-1; METHANOCALDOCOCCUS JANNASCHII; PYROCOCCUS HORIKOSHII; THERMOPLASMA; THERMOPLASMA ACIDOPHILUM; THERMOPLASMA VOLCANIUM;

AROMATIC AMINO ACID; ERYTHROSE 4 PHOSPHATE; ERYTHROSE 4-PHOSPHATE; RIBOSE 5 PHOSPHATE; RIBOSE PHOSPHATE; RIBOSE-5-PHOSPHATE; SUGAR PHOSPHATE;

ARCHAEBACTERIUM; ARTICLE; BIOSYNTHESIS; ENZYMOLOGY; GENE; GENETICS; GENOME; METABOLISM; PENTOSE PHOSPHATE CYCLE; PHYLOGENY;

AMINO ACIDS, AROMATIC; ARCHAEA; GENES, ARCHAEAL; GENOME, ARCHAEAL; PENTOSE PHOSPHATE PATHWAY; PHYLOGENY; RIBOSEMONOPHOSPHATES; SUGAR PHOSPHATES;

EID: 20144364025     PISSN: 14723646     EISSN: None     Source Type: Journal    
DOI: 10.1155/2005/314760     Document Type: Article

References (22)

1. Choquet, C.G., J.C Richards and G.D. Sprott. 1994. Ribose synthesis in methanogenic archaea. Arch. Microbiol. 161:481-488.
2. Daugherty, M., V. Vonstein, R. Overbeek and A. Osterman. 2001. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183:292-300.
3. Eisenreich, W., B. Schwarzkopf and A. Bacher. 1991. Biosynthesis of nucleotides, flavins, and deazaflavins in Methanobacterium thermoautotrophicum. J. Biol. Chem. 266:9622-9631.
4. 13C nuclear magnetic resonance. J. Bacteriol. 156:316-326.
5. Gonzalez, J.M., Y. Masuchi, F.T. Robb, J.W. Ammerman, D.L. Maeder, J. Yanagibayashi, J. Tamaoka and C. Kato. 1998. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 2: 123-130.
6. Ishikawa, K., I. Matsui, F. Payan, C. Cambillau, H. Ishida, Y. Kawarabayasi, H. Kikuchi and A. Roussel. 2002. A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii: characterization and three-dimensional structure. Structure 10:877-886.
7. Martinez-Cruz, L.A., M.K. Dreyer, D.C. Boisvert, H. Yokota, M.L. Martinez-Chanter, R. Kim and S.H. Kim. 2002. Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure 10:195-204.
8. Ogushi, S., M. Ando and D. Tsuru. 1984. Formaldehyde dehydrogenase from Pseudomonas putida: a zinc metalloenzyme. J. Biochem. 96:1587-1591.
9. Reizer, J., A. Reizer and M.H. Saier, Jr. 1997. Is the ribulose monophosphate pathway widely distributed in bacteria? Microbiology 143:2519-2520.
10. Roy, R., M. Swarnalatha, G.J. Schut, D.M. Dunn, R. Weiss and M.W.W. Adams. 1999. Purification and characterization of the tungsten-containing formaldehyde ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus: the third of a putative five-member tungstoenzyme family. J. Bacteriol. 181:1171-1180.
11. Selkov, E., N. Maltsev, G.J. Olsen, R. Overbeek and W.B. Whitman. 1997. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197:GC11-26.
12. Snel, B., G. Lehmann, P. Bork and M.A. Huynen. 2000. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28:3442-3444.
13. Soderberg, T. and R.C. Alver. 2004. Transaldolase of Methanocaldococcus jannaschii. Archaea 1:255-262.
14. Tanaka, N., Y. Kusakabe, K. Ito, T. Yoshimoto and K.T. Nakamura. 2002. Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases. J. Mol. Biol. 324:519-533.
15. Tatusov, R.L., E.V. Koonin and D.J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
16. Tatusov, R.L., D.A. Natale, I.V. Garkavtsev et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
17. Tumbula, D.L, Q. Teng, M.G. Bartlett and W.B. Whitman. 1997. Ribose biosynthesis and evidence for an alternative first step in the common aromatic amino acid pathway in Methanococcus maripaludis. J. Bacteriol. 179:6010-6013.
18. von Mering, C., M. Huynen, D. Jaeggi, S. Schmidt, P. Bork and B. Snel. 2003. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31:258-261.
19. White, R.H. 2004. L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose-1- phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. Biochemistry 43:7618-7627.
20. Vorholt, J.A., C.J. Marx, M.E. Lidstrom and R.K. Thauer. 2000. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182:6645-6650.
21. Yasueda, H., Y. Kawahara and S. Sugimoto. 1999. Bacillus subtilus yckG and yckF encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckH is required for their expression. J. Bacteriol. 181:7154-7160.
22. Yu, J.P., J. Ladapo and W.B. Whitman. 1994. Pathway of glycogen metabolism in Methanococcus maripaludis. J. Bacteriol. 176:325-332.