New insights into short-chain prenyltransferases: structural features, evolutionary history and potential for selective inhibition

Abstract

Isoprenoids form an extensive group of natural products involved in a number of important biological processes. Their biosynthesis proceeds through sequential 1'-4 condensations of isopentenyl diphosphate (C5) with an allylic acceptor, the first of which is dimethylallyl diphosphate (C5). The reactions leading to the production of geranyl diphosphate (C10), farnesyl diphosphate (C15) and geranylgeranyl diphosphate (C20), which are the precursors of mono-, sesqui- and diterpenes, respectively, are catalyzed by a group of highly conserved enzymes known as short-chain isoprenyl diphosphate synthases, or prenyltransferases. In recent years, the sequences of many new prenyltransferases have become available, including those of several plant and animal geranyl diphosphate synthases, revealing novel mechanisms of product chain-length selectivity and an intricate evolutionary path from a putative common ancestor. Finally, there is considerable interest in designing inhibitors specific to short-chain prenyltransferases, for the purpose of developing new drugs or pesticides that target the isoprenoid biosynthetic pathway.

Fig. 1

Elongation reactions catalyzed by short-chain prenyltransferases, along with examples of final products generated by the geranyl diphosphate (GPP), farnesyl diphosphate (FPP), geranylgeranyl diphosphate (GGPP), and farnesylgeranyl diphosphate (FGPP) precursors

Fig. 2

Phylogenetic tree (unrooted) of trans-isoprenyl diphosphate synthases from diverse taxa. Nucleotide sequences were retrieved from Genbank and imported into MEGA4 [91], where they were conceptually translated into proteins. Alignments were performed on the amino acid sequences using ClustalW, as implemented by MEGA4, with default settings except for penalties relating to multiple alignment gap openings and extensions, which were set to 3.0 and 1.8, respectively [92]. The back-translated nucleotide alignment was then used to construct a Neighbor-Joining tree using MEGA4’s default settings, except for gap deletions, where the pairwise deletion option was selected. Bootstrapping was performed on 2,000 pseudoreplicates, and all branches with less than 50% boostrap support were collapsed. For each enzyme or enzyme lineage, residues within the chain-length determination (LCD) region [i.e., the first aspartate-rich motif (“FARM” = DDxxD or DDxooxD) and the five residues upstream from it] are shown as a color-coded sequence, where x = L, I, V or M, and o = any amino acid. Residues at position -4 and -5 relative to the FARM are shown in green, while the residue at position -1 is shown in red. Aspartate residues within the FARM are shown in blue. Accession numbers: GPPS: algae, XM_001691017; Arabidopsis, Y17376; bark beetle, AY953508; grand fir, AF513112; longhorn beetle, not yet deposited; Mentha, AF182828; spruce; EU432048; tomato, DQ286930; GPPS/FPPS: aphid, AY968586; FPPS: Arabidopsis, L46350; bark beetle, AY953507; Drosophila, NM_058032; E. coli, D00694; human, NM_002004; Micrococcus, AB003187; mosquito, XM_308653; nematode, NM_060626; Plasmodium-AY219707; spruce budworm-1, AY954920; spruce budworm-2, AY954919; Trypanosoma, AF386102; yeast, NC_001142; FPPS/GGPPS: Methanothermobacter, S75695; Mycobacterium, NC_000962; GGPPS: Arabidopsis, NM_127943; Drosophila, AF049659; human, NM_004837; Pantoea, D90087; Sulfolobus, NC_007181; Yeast, AY692852; FGPPS: Aeropyrum, AB025791; hexaprenyl diphosphate synthase (HPPS; C30): Micrococcus, AB003188; heptaprenyl diphosphate synthase (HepPPS; C35): Bacillus, EF191544; octaprenyl diphosphate synthase (OPPS; C40): Archeoglobus, AE000782; E. coli, U18997; Trypanosoma, XM_799480; solanesyl diphosphate synthase (SPPS): Arabidopsis, NM_001084371; mouse, NM_019501; Mucor mold, AJ496300; Rhodobacter, AB001997; decaprenyl diphosphate synthase (DPPS; C50): fission yeast, NM_001021183; human, NM_014317; PPPS: aphid, XM_001947162; body louse, DS235241; chicken, XM_418592; Drosophila, NM_170546; Methanosarcina, NC_007355; mosquito, XM_565746; Plasmodium, XM_001349505; Tribolium, XM_968226; wasp, XM_001602302