Functional genomics of plant natural product biosynthesis; shikimate and phenylpropanoid pathways; wood formation
Plants synthesize a vast array of diverse secondary compounds or natural products that serve pivotal adaptive functions including protection against pests, attractants for pollinators, antagonists to other plants, structural components, and signaling molecules However, the vast majority of metabolic pathways leading to their biosynthesis still await discovery. This is especially true for forest trees, but having available the complete Populus genome allows functional genomics studies in this forest tree.
My research aims to understand how carbon flow into diverse branch pathways of natural product biosynthesis is allocated, achieved and regulated. A particular focus lies on the shikimate pathway that connects primary sugar metabolism with the biosynthesis of essential aromatic amino acids. The major carbon sink of the shikimate pathway is the phenylpropanoid pathway branch leading to lignin, which makes up to a third of the dry mass of wood and is the second most abundant biopolymer on earth. However, this pathway also branches off to myriad other phenolic compounds with diverse and pivotal functions in plant chemical ecology. The mechanisms that assure appropriate carbon allocation to the diverse branch pathways and the biosynthetic routes leading to the numerous derivatives are still largely unknown.
To address this problem we use bioinformatic approaches to exploit the available Populus genome sequence as well as whole transcriptome and proteome abundance data. These tools can be used to identify candidate genes and develop hypotheses regarding their biochemical and physiological functions. Thus identified candidate genes are then being analyzed experimentally using the tools of molecular biology, reverse biochemistry, and reverse genetics to test the in silico generated hypotheses in the lab.
