Focused and nontargeted approaches were used to assess the impact associated with introduction of new high-flux pathways in Arabidopsis thaliana by genetic engineering. Transgenic A. thaliana plants expressing the entire biosynthetic pathway for the tyrosine-derived cyanogenic glucoside dhurrin as accomplished by insertion of CYP79A1, CYP71E1, and UGT85B1 from Sorghum bicolor were shown to accumulate 4% dry-weight dhurrin with marginal inadvertent effects on plant morphology, free amino acid pools, transcriptome, and metabolome. In a similar manner, plants expressing only CYP79A1 accumulated 3% dry weight of the tyrosine-derived glucosinolate, p-hydroxybenzylglucosinolate with no morphological pleitropic effects. In contrast, insertion of CYP79A1 plus CYP71E1 resulted in stunted plants, transcriptome alterations, accumulation of numerous glucosides derived from detoxification of intermediates in the dhurrin pathway, and in loss of the brassicaceae-specific UV protectants sinapoyl glucose and sinapoyl malate and kaempferol glucosides. The accumulation of glucosides in the plants expressing CYP79A1 and CYP71E1 was not accompanied by induction of glycosyltransferases, demonstrating that plants are constantly prepared to detoxify xenobiotics. The pleiotrophic effects observed in plants expressing sorghum CYP79A1 and CYP71E1 were complemented by retransformation with S. bicolor UGT85B. These results demonstrate that insertion of high-flux pathways directing synthesis and intracellular storage of high amounts of a cyanogenic glucoside or a glucosinolate is achievable in transgenic A. thaliana plants with marginal inadvertent effects on the transcriptome and metabolome.DNA microarrays ͉ metabolic engineering ͉ metabolite profiling ͉ channeling ͉ substantial equivalence M etabolic engineering offers the possibility to design plants that produce desired compounds (1-3). Knowledge of the impact of insertion of metabolic pathways on preexisting metabolic pathways is typically scarce, and is assessed by targeted approaches, but not by more global and unbiased approaches. We have previously reported transfer of the entire pathway for synthesis of the tyrosine-derived cyanogenic glucoside dhurrin from Sorghum bicolor to Arabidopsis thaliana by coexpression of three S. bicolor cDNAs: two multifunctional cytochromes P450, CYP79A1 and CYP71E1, and a family 1 glucosyltransferase, UGT85B1 (Fig. 1). The transgenic A. thaliana plants accumulated up 4% of plant dry matter of dhurrin (4). Transgenic A. thaliana plants in which only CYP79A1 was introduced accumulated up to 3% dry matter of the tyrosine derived p-hydroxybenzylglucosinolate, a glucosinolate that does not occur naturally in A. thaliana (5). The accumulation of tyrosine derived p-hydroxybenzylglucosinolate in A. thaliana is the result of metabolic crosstalk, where the p-hydroxyphenylacetaldoxime produced by CYP79A1 is efficiently used by the post-oximemetabolizing enzymes CYP83B1 or CYP83A1 in the endogenous glucosinolate biosynthetic pathway (5, 6) (Fig. 1).In this study,...