Global gene expression and secondary metabolite changes in Arabidopsis thaliana ABI4 over-expression lines

Despite numerous studies on ABI4, its role in plant secondary metabolism has not been fully investigated. Here, we used metabolite profiling together with transcriptome analysis to demonstrate that ABI4 transcript levels regulate a host of secondary metabolite pathways and growth modalities in ABI4 over-expression (ABI4_OE) lines of Arabidopsis thaliana. This strategy provided a unique and comprehensive overview of the regulation of metabolic shifts in response to ABI4 transcription. We show that enhancement of ABI4 transcript levels changed seed proanthocyanidin (PA), flavonoid, and carotenoid levels in ABI4_OE seeds and 30-day-old shoots, as well as the expression of genes encoding enzymes involved in the production of these and other secondary metabolites in ABI4_OE shoots. In seeds, PA accumulated in very large uneven patches, which was dramatically different from the even distribution of PA in wild-type seeds. Shoots of ABI4_OE lines also exhibited altered expression of a range of genes involved in several aspects of plant development, including hormone and cell-wall synthesis. Alteration of such disparate secondary metabolite pathways, along with hormone and developmental pathways, suggests that ABI4 is a master regulator integrating these compounds with plant development.