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

Soderberg, Tim

doi:https://doi.org/10.1155/2005/314760

Archaea

On this page

Abstract References Copyright Related Articles

Research Article | Open Access

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

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

Tim Soderberg¹

Received07 Jun 2004

Accepted15 Sept 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

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
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
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
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
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
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
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
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
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
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
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
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
T. Soderberg and R.C. Alver, “Transaldolase of Methanocaldococcus jannaschii,” Archaea, vol. 1, pp. 255–262, 2004.
View at: Google Scholar
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
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
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
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
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
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
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
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
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

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.

PDF Download Citation Order printed copies

Views

991

Downloads

1639

Citations