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.
Highlights
The pentose phosphate pathway (PPP) is a ubiquitous metabolic pathway in bacteria and eukaryotes
Ubiquitous in archaeal genomes are most of the genes for nucleotide biosynthesis, including putative genes for phosphoribosylpyrophosphate (PRPP) synthase (COG 0462), orotate phosphoribosyltransferase (COG 0461) and glutamine phosphoribosyl amidotransferase (COG 0034), the key enzymes responsible for incorporating R5P into nucleotides
The question becomes how Ru5P is synthesized by those archaea that lack a complete set of nonoxidative PPP (NOPPP) orthologs
Summary
The pentose phosphate pathway (PPP) is a ubiquitous metabolic pathway in bacteria and eukaryotes. The authors proposed that R5P synthesis in methanococci occurs solely via the NOPPP enzymes acting in the ‘reverse’ direction (F6P and GAP to Ru5P), and not by oxidative decarboxylation of G6P. This hypothesis was further supported by studies with Methanococcus voltae (Choquet et al 1994) and M. maripaludis (Tumbula et al 1997), in which 13C labeling patterns were consistent with R5P and E4P synthesis via the NOPPP. The same studies revealed labeling patterns in phenylalanine and tyrosine that were inconsistent with the biosynthesis of these aromatic amino acids starting from E4P, calling into question the role of E4P and the NOPPP in these species
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