Plant secondary or "specialized" metabolites play an important role in plant survival, often as defense chemicals, and are the predominant natural sources of drugs for human health because of their chemical diversity and biosynthetic complexity. As a consequence, the biosynthesis and regulation of plant specialized metabolism have been intensively studied in a number of model and non-model plant species. Here, we review what is currently known about the transcriptional regulators and pathway enzymes that contribute to the chemical diversity and biosynthetic complexity of two of the three major groups of plant specialized metabolites, the phenylpropanoids and the nitrogen-containing alkaloids. For the latter, we will focus on aromatic amino acid-derived alkaloids that have been extensively studied for their regulation and biosynthesis. They include the amine-derived terpenoid indole alkaloids, the free indole-derived benzoxazinoids, and the oximederived aromatic compounds, such as the tyrosine-derived cyanogenic glycosides, indole glucosinolates, and sulfur-containing indole alkaloids. In addition, we will discuss the possible phylogenetic conservation of the transcriptional regulators of phenylpropanoid metabolism in defense.
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