COMPARATIVE GENOMICS OF THE SHIKIMATE PATHWAY IN ARABIDOPSIS, POPULUS TRICHOCARPA AND ORYZA SATIVA: SHIKIMATE PATHWAY GENE FAMILY STRUCTURE AND IDENTIFICATION OF CANDIDATES FOR MISSING LINKS IN PHENYLALANINE BIOSYNTHESIS

摘要

The great majority of aromatic compounds and their precursors are synthesized via the shikimate and its numerous branch pathways. This pathway, found in bacteria, fungi, and plants, connects primary carbohydrate metabolism with the biosynthesis of the three aromatic amino acids tryptophan, tyrosine, and phenylalanine. These three amino acids, essential for the animal diet, serve in plants as precursors for innumerable secondary metabolites ranging from alkaloids to phenylpropanoids. Shikimate pathway derived metabolites such as flavonoids, monolignols, and soluble and wall-bound phenolics represent the main metabolic sink for phenylalanine after its entry into the phenylpropanoid pathway, catalyzed by the combined actions of phenylalanine ammonia-lyase (PAL) and cinnamate-4-hydroxylase (C4H) to generate p-coumarate. It is estimated that 20% of the total carbon fixed in plants growing under standard conditions flows through this pathway, and the myriad of shikimate-derived compounds play vital roles in plant defence against biotic and abiotic stresses, plant development and structure, and plant-environment interaction. Most of the genes and corresponding enzymes in the shikimate pathway have been characterized in model plants such as Arabidopsis and tomato, and there is evidence from these and other plant systems that activity of the pathway, as measured by changes in gene expression, is coordinated with demand for phenylalanine entry into phenylpropanoid metabolism. However, the genes encoding two key steps in phenylalanine biosynthesis, prephenate aminotransferase (PNT) and arogenate dehydratase (ADT) have yet to be identified, and the specific corresponding enzymes remain unknown.