Research Article | Open Access
Tim Soderberg, "Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes", Archaea, vol. 1, Article ID 314760, 6 pages, 2005. https://doi.org/10.1155/2005/314760
Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes
A phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (PPP), the ribulose monophosphate (RuMP) pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the PPP genes in archaea. Genomic and biochemical evidence suggests that three archaeal species (Methanocaldococcus jannaschii, Thermoplasma acidophilum and Thermoplasma volcanium) produce ribose-5-phosphate via the nonoxidative PPP (NOPPP), whereas nine species apparently lack an NOPPP but may employ a reverse RuMP pathway for pentose synthesis. One species (Halobacterium sp. NRC-1) lacks both the NOPPP and the RuMP pathway but may possess a modified oxidative PPP (OPPP), the details of which are not yet known. The presence of transketolase in several archaeal species that are missing the other two NOPPP genes can be explained by the existence of differing requirements for erythrose-4-phosphate (E4P) among archaea: six species use transketolase to make E4P as a precursor to aromatic amino acids, six species apparently have an alternate biosynthetic pathway and may not require the ability to make E4P, and one species (Pyrococcus horikoshii) probably does not synthesize aromatic amino acids at all.
- C.G. Choquet, J.C Richards, and G.D. Sprott, “Ribose synthesis in methanogenic archaea,” Arch. Microbiol., vol. 161, pp. 481–488, 1994.
- M. Daugherty, V. Vonstein, R. Overbeek, and A. Osterman, “Archaeal shikimate kinase, a new member of the GHMP-kinase family,” J. Bacteriol., vol. 183, pp. 292–300, 2001.
- W. Eisenreich, B. Schwarzkopf, and A. Bacher, “Biosynthesis of nucleotides, flavins, and deazaflavins in Methanobacterium thermoautotrophicum,” J. Biol. Chem., vol. 266, pp. 9622–9631, 1991.
- I. Ekiel, I.C.P. Smith, and G.D. Sprott, “Biosynthetic pathways in Methanospirillum hungatei as determined by 13C nuclear magnetic resonance,” J. Bacteriol., vol. 156, pp. 316–326, 1983.
- J.M. Gonzalez, Y. Masuchi, and Y. Masuchi, “Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough.,” Extremophiles, vol. 2, pp. 123–130, 1998.
- K. Ishikawa, I. Matsui, and I. Matsui, “A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii: characterization and three-dimensional structure,” Structure, vol. 10, pp. 877–886, 2002.
- L.A. Martinez-Cruz, M.K. Dreyer, D.C. Boisvert, H. Yokota, M.L. Martinez-Chanter, R. Kim, and S.H. Kim, “Crystal structure of MJ1247 protein from M. jannaschii at 2.0 Å resolution infers a molecular function of 3-hexulose-6-phosphate isomerase.,” Structure, vol. 10, pp. 195–204, 2002.
- S. Ogushi, M. Ando, and D. Tsuru, “Formaldehyde dehydrogenase from Pseudomonas putida: a zinc metalloenzyme,” J. Biochem., vol. 96, pp. 1587–1591, 1984.
- J. Reizer, A. Reizer, and M.H. Saier, “Is the ribulose monophosphate pathway widely distributed in bacteria?” Microbiology, vol. 143, pp. 2519–2520, 1997.
- R. Roy, M. Swarnalatha, G.J. Schut, D.M. Dunn, R. Weiss, and M.W.W. Adams, “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., vol. 181, pp. 1171–1180, 1999.
- E. Selkov, N. Maltsev, G.J. Olsen, R. Overbeek, and W.B. Whitman, “A reconstruction of the metabolism of Methanococcus jannaschii from sequence data,” Gene, vol. 197, pp. GC11–26, 1997.
- B. Snel, G. Lehmann, P. Bork, and M.A. Huynen, “STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene,” Nucleic Acids Res., vol. 28, pp. 3442–3444, 2000.
- T. Soderberg and R.C. Alver, “Transaldolase of Methanocaldococcus jannaschii,” Archaea, vol. 1, pp. 255–262, 2004.
- N. Tanaka, Y. Kusakabe, K. Ito, T. Yoshimoto, and K.T. Nakamura, “Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases,” J. Mol. Biol., vol. 324, pp. 519–533, 2002.
- R.L. Tatusov, E.V. Koonin, and D.J. Lipman, “A genomic perspective on protein families,” Science, vol. 278, pp. 631–637, 1997.
- R.L. Tatusov, D.A. Natale, I.V. Garkavtsev et al., “The COG database: new developments in phylogenetic classification of proteins from complete genomes,” Nucleic Acids Res., vol. 29, pp. 22–28, 2001.
- D.L. Tumbula, Q. Teng, M.G. Bartlett, and W.B. Whitman, “Ribose biosynthesis and evidence for an alternative first step in the common aromatic amino acid pathway in Methanococcus maripaludis,” J. Bacteriol., vol. 179, pp. 6010–6013, 1997.
- C. von Mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork, and B. Snel, “STRING: a database of predicted functional associations between proteins,” Nucleic Acids Res., vol. 31, pp. 258–261, 2003.
- J.A. Vorholt, C.J. Marx, M.E. Lidstrom, and R.K. Thauer, “Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol,” J. Bacteriol., vol. 182, pp. 6645–6650, 2000.
- R.H. White, “L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose-1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii,” Biochemistry, vol. 43, pp. 7618–7627, 2004.
- H. Yasueda, Y. Kawahara, and S. Sugimoto, “Bacillus subtilusyckG and yckF encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckH is required for their expression,” J. Bacteriol., vol. 181, pp. 7154–7160, 1999.
- J.P. Yu, J. Ladapo, and W.B. Whitman, “Pathway of glycogen metabolism in Methanococcus maripaludis,” J. Bacteriol., vol. 176, pp. 325–332, 1994.
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