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. 2013 Dec 10;2:e00672.
doi: 10.7554/eLife.00672.

Discovery of a Metabolic Alternative to the Classical Mevalonate Pathway

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Free PMC article

Discovery of a Metabolic Alternative to the Classical Mevalonate Pathway

Nikki Dellas et al. Elife. .
Free PMC article

Abstract

Eukarya, Archaea, and some Bacteria encode all or part of the essential mevalonate (MVA) metabolic pathway clinically modulated using statins. Curiously, two components of the MVA pathway are often absent from archaeal genomes. The search for these missing elements led to the discovery of isopentenyl phosphate kinase (IPK), one of two activities necessary to furnish the universal five-carbon isoprenoid building block, isopentenyl diphosphate (IPP). Unexpectedly, we now report functional IPKs also exist in Bacteria and Eukarya. Furthermore, amongst a subset of species within the bacterial phylum Chloroflexi, we identified a new enzyme catalyzing the missing decarboxylative step of the putative alternative MVA pathway. These results demonstrate, for the first time, a functioning alternative MVA pathway. Key to this pathway is the catalytic actions of a newly uncovered enzyme, mevalonate phosphate decarboxylase (MPD) and IPK. Together, these two discoveries suggest that unforeseen variation in isoprenoid metabolism may be widespread in nature. DOI: http://dx.doi.org/10.7554/eLife.00672.001.

Keywords: Archaea; Chloroflexi; Isopentenyl diphosphate; Mevalonate pathway; Mevalonate phosphate decarboxylase; Plants.

Conflict of interest statement

The authors declare that no competing interests exist.

Figures

Figure 1.
Figure 1.. The classical and alternative MVA pathways.
Both branches of the MVA pathway begin with acetyl-CoA (and acetoacetyl-CoA) and proceed through a series of enzymatic reactions involving 3-hydroxy-3-methylglutary-CoA Synthase (HMGS), 3-hydroxy-3-methylglutary-CoA Reductase (HMGR, the presumed early rate-limiting step), and mevalonate kinase (MVK) before branching. At the bifurcation, the canonical MVA pathway, highlighted by light blue arrows, guides MVAP (3) through an additional phosphorylation reaction followed by a phosphorylation-dependent decarboxylation carried out by phosphomevalonate kinase (PMK) and diphosphomevalonate decarboxylase (MDD), respectively. The alternative MVA pathway, highlighted with light brown arrows, hypothetically decarboxylates MVAP (3) prior to the phosphorylation reaction carried out by IPK but the former step has not been discovered until now (Grochowski et al., 2006). The enzymes MVK, PMK, MDD, and IPK all consume ATP during catalysis. All enzymes are shown in green type. Statins serve as inhibitors of HMGR as highlighted. DOI: http://dx.doi.org/10.7554/eLife.00672.003
Figure 2.
Figure 2.. Phylogenetic distribution of IPK across the three domains of life.
Maximum likelihood tree of selected IPK protein sequences. Eukaryotes are highlighted with blues, selected archaeal clades with grays and a small group of bacteria with purple. The tree is anchored by several bacterial fosfomycin kinases. See Figure 2—source data 1 for an alignment of IPK homologs. See Figure 2—source data 2 for a table of IPK homolog sequences. DOI: http://dx.doi.org/10.7554/eLife.00672.004
Figure 3.
Figure 3.. Fluorescence thermal shift assays of Roseiflexus castenholzii MDD-like MPD.
(A) Thermograms for R. castenholzii MPD in 100 mM buffer (pH 3.0–3.8 citric acid; pH 4.0–4.8 sodium acetate; pH 5.0–5.8 sodium citrate; pH 6.0–6.8 sodium cacodylate; pH 7.0–7.8 sodium HEPES; pH 8.0–8.8 Tris-HCl; pH 9.0–11.0 CAPSO) colored from red to violet (acidic to alkaline pH depicted in the inset). (B) Negative derivatives of the thermograms (−dF/dT) color-coded as in (A). (C) Tms for each of the curves show in (A) and (B) plotted as a function of pH. R. castenholzii MPD was unfolded from pH 2.2 to 2.8 at 20°C (data now shown). DOI: http://dx.doi.org/10.7554/eLife.00672.014
Figure 4.
Figure 4.. In vitro reconstitution and GC-MS analysis of the alternative and classical MVA pathways.
(A) Terminal steps of the MVA pathways shown with enzymes of the alternative (orange) and classical (blue) pathways depicted as arrows. The putative neofunctionalization of MDD to MPD is highlighted by a grey arrow. (B) In vitro assays include either the alternative or the classical enzymes to produce IPP (1) (as shown in panel A) as well as all downstream enzymes, including isopentenyl phosphate isomerase (IPPI) to produce DMAPP (2), farnesyl diphosphate synthase (FPPS) to produce farnesyl diphosphate (FPP, 6) and tobacco 5-epi-aristolochene synthase (TEAS) to produce the sesquiterpene product, 5-EA (7). Products are separated by GC and detected by MS ionization and fragmentation. Enzymes used are highlighted in turquoise type. (C) Results of the in vitro reconstitutions of various enzyme combinations. The y-axis of the graph represents combinations of enzymes shown in panel A and panel B and the % conversion to the expected sesquiterpene end product, 5-EA (7) shown as grey bars along the x-axis. Abbreviations of organisms are as follows: Bf = Branchiostoma floridae , At = Arabidopsis thaliana, Ss = Sulfolobus solfataricus, and Rc = Roseiflexus castenholzii. Note, RcMPD is colored both orange and blue on the y-axis, depending on whether it is being tested as an MDD (blue) or an MPD (orange). DOI: http://dx.doi.org/10.7554/eLife.00672.015
Figure 5.
Figure 5.. Structural comparisons of a bona fide MDD and MPD.
Interactions between the terminal phosphate of 6F-MVAPP and the surrounding amino acid residues from the crystal structure of S. epidermidis MDD (PDB ID 3QT7(Barta et al., 2011)) and the 3D model of MPD from R. castenholzii. (A) S. epidermidis MDD has multiple interactions with the diphosphate of MVAPP (5). Atoms are colored by type with carbon gold. (B) The active site model of R. castenholzii MPD lacks many of the key interactions shown by S. epidermidis MDD in panel A. Atoms are colored by type with carbon green. (C) Interactions between the monophosphate of modeled 6F-MVAP and the surrounding amino acids in a superposition of the modeled R. castenholzii MPD, backbone atoms and carbon colored green, on the crystal structure of S. epidermidis MDD, backbone atoms and carbon colored gold. In R. castenholzii MPD, two divergent side chains, Arg83 and Lys161, putatively provide additional electrostatic interactions with the single phosphate group of MVAP (3). These amino acid side chains would clash with the second phosphate of MVAPP (5). These models suggest that the predicted active site topology of R. castenholzii MPD facilitates substrate recognition of MVAP (3) through complementary charged and polarized hydrogen bonds and excludes MVAPP (5) through steric incompatibility with its second phosphate. DOI: http://dx.doi.org/10.7554/eLife.00672.016

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