Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes

Abstract

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.chloroplast ͉ deoxyxylulose 5-phosphate ͉ endosymbiosis ͉ mevalonate ͉ phylogeny

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

“…That prediction fares quite well. of acetyl-CoA (Lange et al 2000). Not only do the isoprene side chain pathways differ in the two groups, the proton-and electron-transferring aromatic heads of the quinones also differ in archaebacteria and eubacteria: although some archaebacteria possess menaquinone and ubiquinone like eubacteria, others use sulphur-containing heterocyclics such as the benzothiophenes of Sulfolobus and Acidianus (Schü tz et al 2000), whereby the methanogens use methanophenazine, which is not a quinone at all (Berry (2002), q.v.…”

“…for quinone structural comparisons). Interestingly, a key enzyme of the MVA pathway, 3-hydroxy-3-methylglutaryl-CoA synthase is distantly related to b-ketoacyl-acyl carrier protein synthase III of eubacteria (Lange et al 2000), which catalyses a similar condensation reaction to produce the fatty acid precursor acetoacetyl-ACP from acetyl-ACP and malonyl-CoA as substrates, indicating the presence of an ancestral acetyl-CoA condensing protein in the non-free-living universal ancestor. Furthermore, DXP synthase of the DXP isoprenoid route is distantly related to PFOR, a ferredoxin-dependent enzyme catalysing the C 2 !…”

“…The evolutionary basis for the fundamental differences that distinguish eubacteria and archaebacteria, but which more or less uniformly unite the respective groups, could be sought in the age of biochemical discovery during the persistence of proto-eubacterial and protoarchaebacterial lineages living within the confines of their energy-laden mineral incubator. Such differences would include their use of many fundamentally different cofactors such as pterin derivatives versus tetrahydrofolate, coenzyme B, methanofuran, coenzyme F420, coenzyme M and cobamids in many archaebacteria (see DiMarco et al 1990;Thauer 1998;White 2001), their use of different pathways for the same metabolic intermediates such as IPP (Lange et al 2000) or their differences in purine biosynthesis (White 1997), their use (archaebacteria) or disuse (eubacteria) of small nucleolar RNAs for the modification of ribosomes (Omer et al 2000), the differences between their DNA maintenance and repair machineries (Tye 2000), the differences between their transcriptional regulatory apparatus (Thomm 1996;Bell et al 2001) and RNA polymerases (Langer et al 1995;Bell & Jackson 1998), their quinones (Schü tz et al 2000;Berry 2002), or, and what is probably the most important point for this paper, the differences between their membrane lipid biosynthetic pathways and cell-wall constituents (Kandler 1982). Many other such differences could be listed.…”

Maize cDNAs Expressed in Endosperm Encode Functional Farnesyl Diphosphate Synthase with Geranylgeranyl Diphosphate Synthase Activity

“…With more than 30,000 identified compounds, isoprenoids are the oldest, most abundant, and structurally diverse natural products (Lange et al, 2000;Kharel and Koyama, 2003). In plants, isoprenoids and their derivatives are involved in a number of important processes, including photosynthesis and photoprotection, defense, regulation of growth and development, and attracting animals involved in pollination and seed dispersion (DellaPenna, 1999).…”

Isoprenoid biosynthesis in the diatoms Rhizosolenia setigera (Brightwell) and Haslea ostrearia (Simonsen)

“…Many authors have studied the distribution of the MVA and MEP pathways within a large number of organisms by incorporation of 13 C-or 2 H-labeled precursors (for reviews see refs. 1, 3, and 4), by use of highly specific inhibitors of the MVA and MEP pathways (5, 6), or by measuring the distribution of the genes of both pathways (7,8). Jux and coworkers (9) demonstrated that natural 13 C͞ 12 C isotope ratios of individual lipids could also be used to distinguish between the pathways.…”