Expression Profile of Genes Involved in Isoprenoid Biosynthesis in the Marine Diatom <i>Phaeodactylum tricornutum</i>

Abstract

The marine diatom Phaeodactylum tricornutum is expected to be a source of hydrocarbons and carotenoids that are synthesized via isoprenoid precursor biosynthesis pathways such as the mevalonate (MVA) and the 2-C-methyl-D-erythritol phosphate (MEP) pathways, because the molecular biotechnological techniques for metabolic engineering have been established. In this study, we investigated the expression profiles of the genes, including those in the MVA and MEP pathways, under various culture conditions using RNA-seq analysis to obtain information useful for the metabolic engineering and development of endogenous promoters that can highly drive the expression of transgenes in P. tricornutum. The expression levels of the genes in the MVA pathway, except for the 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) gene, were low under all the conditions tested, and the expression levels of the 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (CMK) and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (MDS) genes in the MEP pathway were relatively low. Eleven genes with high expression levels, including the V-type proton ATPase subunit C-like gene, which are potential sources of endogenous promoters in P. tricornutum, were selected. These results are expected to provide useful information for the metabolic engineering of P. tricornutum.

An exception among diatoms: unique organization of genes involved in isoprenoid biosynthesis in Rhizosolenia setigera CCMP 1694

“…setigera (Ferriols et al ., ) and the non‐HBI‐producing diatom P . tricornutum (Kira et al ., ) using BLAST (Altschul et al ., ). Although nearly all isoprenoid biosynthesis‐related genes present in P .…”

“…With the initial objective of finding candidate genes that encode for enzymes that could potentially catalyze the final steps in HBI biosynthesis, we set out to identify and compare genes involved in isoprenoid biosynthesis from inhouse transcriptomic and genomic databases of the HBIproducing diatom R. setigera (Ferriols et al, 2015) and the non-HBI-producing diatom P. tricornutum (Kira et al, 2016) using BLAST (Altschul et al, 1990). Although nearly all isoprenoid biosynthesis-related genes present in P. tricornutum had corresponding homologues in R. setigera, one distinct observation was that the SQS homologue in our R. setigera database appeared as a separate contig from two independent IDI homologues (Table S2).…”