Archaea

Archaea / 2005 / Article

Research Article | Open Access

Volume 1 |Article ID 314760 | https://doi.org/10.1155/2005/314760

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

Received07 Jun 2004
Accepted15 Sep 2004

Abstract

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.

References

  1. C.G. Choquet, J.C Richards, and G.D. Sprott, “Ribose synthesis in methanogenic archaea,” Arch. Microbiol., vol. 161, pp. 481–488, 1994. View at: Google Scholar
  2. 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. View at: Google Scholar
  3. 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. View at: Google Scholar
  4. 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. View at: Google Scholar
  5. 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. View at: Google Scholar
  6. 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. View at: Google Scholar
  7. 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. View at: Google Scholar
  8. S. Ogushi, M. Ando, and D. Tsuru, “Formaldehyde dehydrogenase from Pseudomonas putida: a zinc metalloenzyme,” J. Biochem., vol. 96, pp. 1587–1591, 1984. View at: Google Scholar
  9. J. Reizer, A. Reizer, and M.H. Saier, “Is the ribulose monophosphate pathway widely distributed in bacteria?” Microbiology, vol. 143, pp. 2519–2520, 1997. View at: Google Scholar
  10. 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. View at: Google Scholar
  11. 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. View at: Google Scholar
  12. 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. View at: Google Scholar
  13. T. Soderberg and R.C. Alver, “Transaldolase of Methanocaldococcus jannaschii,” Archaea, vol. 1, pp. 255–262, 2004. View at: Google Scholar
  14. 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. View at: Google Scholar
  15. R.L. Tatusov, E.V. Koonin, and D.J. Lipman, “A genomic perspective on protein families,” Science, vol. 278, pp. 631–637, 1997. View at: Google Scholar
  16. 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. View at: Google Scholar
  17. 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. View at: Google Scholar
  18. 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. View at: Google Scholar
  19. 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. View at: Google Scholar
  20. 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. View at: Google Scholar
  21. 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. View at: Google Scholar
  22. J.P. Yu, J. Ladapo, and W.B. Whitman, “Pathway of glycogen metabolism in Methanococcus maripaludis,” J. Bacteriol., vol. 176, pp. 325–332, 1994. View at: Google Scholar

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


More related articles

 PDF Download Citation Citation
 Order printed copiesOrder
Views438
Downloads1052
Citations

Related articles