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. 2005 May;1(5):347-52.
doi: 10.1155/2005/314760.

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

Tim Soderberg  1
Affiliations

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

Tim Soderberg. Archaea. 2005 May.

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.

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Figures

Figure 1.
Figure 1.
The pentose phosphate pathway (PPP). Abbreviations: G6P = glucose-6-phosphate; G6PDH = glucose-6-phosphate dehydrogenase; 6PGL = 6-phosphoglucono-δ-lactone; 6PGLase = 6-phosphoglucono-δ-lactonase; 6PG = 6-phosphogluconate; 6PGDH = 6-phosphogluconate dehydrogenase; Ru5P = ribulose-5-phosphate; Ru5PE = ribulose-5-phosphate-3-epimerase; R5PI = ribose-5-phosphate isomerase; R5P = ribose-5-phosphate; X5P = xylulose-5-phosphate; TK = transketolase; S7P = sedoheptulose-7-phosphate; GAP = glyceraldehyde-3-phosphate; TAL = transaldolase; E4P = erythrose-4-phosphate; and F6P = fructose-6-phosphate.
Figure T1.
Figure T1.
Phylogenetic patterns of archaeal gene orthologs from the pentose phosphate pathway (PPP) and the ribulose monophosphate (RuMP) pathway. GenBank accession numbers are listed for each ortholog.
Figure 2.
Figure 2.
The reactions of the ribulose monophosphate (RuMP) pathway. Abbreviations: Ru5P = ribulose-5-phosphate; HPS = 3-hexulose-6-phosphate synthase; Hu6P = 3-hexulose-6-phosphate; PHI = 3-hexulose-6-phosphate isomerase; and F6P = fructose-6-phosphate.
Figure T2.
Figure T2.
Phylogenetic distribution of the novel archaeal chorismate biosynthesis pathway genes (White 2004) compared with the first two steps of classical chorismate biosynthesis and transketolase. GenBank accession numbers are listed for each ortholog.
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