Solanesyl diphosphate (SPP) is regarded as the precursor of the side-chains of both plastoquinone and ubiquinone in Arabidopsis thaliana. We previously analyzed A. thaliana SPP synthase (At-SPS1) (Hirooka et al., Biochem. J., 370, 679-686 (2003)). In this study, we cloned a second SPP synthase (At-SPS2) gene from A. thaliana and characterized the recombinant protein.Kinetic analysis indicated that At-SPS2 prefers geranylgeranyl diphosphate to farnesyl diphosphate as the allylic substrate. Several of its features, including the substrate preference, were similar to those of At-SPS1. These data indicate that At-SPS1 and At-SPS2 share their basic catalytic machinery. Moreover, analysis of the subcellular localization by the transient expression of green fluorescent protein-fusion proteins showed that At-SPS2 is transported into chloroplasts, whereas At-SPS1 is likely to be localized in the endoplasmic reticulum in the A. thaliana cells. It is known that the ubiquinone side-chain originates from isopentenyl diphosphate derived from the cytosolic mevalonate pathway, while the plastoquinone side-chain is synthesized from isopentenyl diphosphate derived from the plastidial methylerythritol phosphate pathway. Based on this information, we propose that At-SPS1 contributes to the biosynthesis of the ubiquinone side-chain and that At-SPS2 supplies the precursor of the plastoquinone side-chain in A. thaliana.Key words: isoprenoid; prenyltransferase; nonaprenyl diphosphate; plastoquinone; ubiquinone Plants have two major prenylquinones, plastoquinone and ubiquinone. 1) Although both share the structural feature of a trans-polyprenyl tail attached to the benzoquinone skeleton and have common oxidationreduction properties, their subcellular localization and biochemical roles are distinct. Plastoquinone exists in the thylakoid membrane of the chloroplast and acts as an electron carrier in the photosynthetic electron transfer reaction,2) whereas ubiquinone exists in the inner membrane of the mitochondrion and transfers electrons in the respiratory chain reaction.3)The hydrophobic tails of prenylquinones are C 30 -C 50 in length and serve as membrane anchors. The lengths of the polyprenyl side-chains differ between plastoquinone and ubiquinone, and even among plant species.4) It is thought that these polyprenyl chains are derived from C 30 -C 50 prenyl diphosphates formed by the consecutive condensation of isopentenyl diphosphate (IPP; C 5 ) with allylic diphosphate in the trans-configuration.5) As for the enzymes giving these precursors, several genes isolated from microorganisms have been well characterized, [6][7][8] but information about the plant-origin enzymes has been limited. Recently, we succeeded in the molecular cloning of Arabidopsis thaliana solanesyl diphosphate (SPP; C 45 ) synthase (At-SPS1; formerly designated At-SPS), which catalyzes the trans-type condensation of IPP to yield the C 45 product. 9) Enzymological analysis indicated that At-SPS1 utilizes both farnesyl diphosphate (FPP; C 15 ) and geranylgeranyl di...