Expression Profile of Genes Involved in Isoprenoid Biosynthesis in the Marine Diatom Phaeodactylum tricornutum

Marine diatoms are major groups of unicellular photosynthetic eukaryotes (Mann and Droop, 1996). Diatoms are of broad interest for basic studies of the ecosystem, evolution, and metabolism due to their enormous contribution to primary production on Earth (Nelson et al., 1995), complex evolutionary history as secondary endosymbionts (Falkowski et al., 2004), and their unique ability to produce silica-based cell walls (Martin-Jézéquel et al., 2000). In addition, diatoms represent a potential source of sustainable products such as hydrocarbon-based biofuel precursors that could serve as a solution to the energy crisis and environmental issues (Wijffels and Barbosa, 2010). Diatoms have also been considered a potential source of commercial applications because they produce bioactive compounds such as carotenoids that are beneficial to human health through their excellent antioxidant activity (Van Den Berg et al., 2000; Pulz and Gross, 2004). In land plants and diatoms, hydrocarbons (e.g., squalene) and carotenoids are synthesized via isoprenoid precursor biosynthesis pathways such as the mevalonate (MVA) and 2-C-methyl-D-erythritol phosphate (MEP) pathways, respectively (Lohr et al., 2012; Fabris et al., 2014). Potential MVA and MEP pathways in Pennales Phaeodactylum tricornutum are summarized in Fig. 1 (Lohr et al., 2012; Hemmerlin, 2013; Vranová et al., 2013; Fabris et al., 2014). To enhance the production of hydrocarbons and carotenoids, overexpression of the 3-hydroxy-3methylglutaryl-coenzyme A reductase (HMGR) gene in the MVA pathway and the 1-deoxy-D-xylulose 5-phosphate synthase (DXS), 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), and 1-hydroxy-2-methyl-2-(E)butenyl 4-diphosphate reductase (HDR) genes in the MEP pathway has been reported, because these enzymes are thought to be the major rate-limiting enzymes in plants (Lohr et al., 2012). For example, the overexpression of the HMGR or DXS genes has resulted in increased phytosterols and carotenoids in tomato, respectively (Enfissi et al., 2005). In diatoms, introducing the endogenous DXS gene to P. tricornutum resulted in an increase in the amount of carotenoids such as fucoxanthin, diadinoxanthin, and -carotene (Eilers et al., 2015). On the other hand, it was reported that control of the MVA and MEP pathways occurs mainly at the transcription level in plants (Vranová et al., 2013). This issue suggests that analyzing the expression profiles of genes in both pathways using quantitative RNA-seq is important for selecting target genes for overexpression. However, the expression profiles of the genes in both pathways of diatoms have not been fully investigated, although the expressed sequence