Predictive Models of Regulatory and Metabolic Pathway for Monolignol Biosynthesis

Full genome information is an essential starting point for systems biology approaches to understanding biosynthetic processes such as the formation of the secondary cell wall. Lignin is a major component of the secondary wall and is a major barrier to the utilization of biomass for energy, papermaking, and forage digestibility.  A systems-level quantitative model of lignin biosynthesis would lead to a better understanding of cell wall formation, providing more precise strategies to improve the production of energy and biomaterials from wood.  We developed a mechanistic model of the catalytic functions of the 4CL family of enzymes (Ptr4CL3 and Ptr4CL5) implicated in monolignol biosynthesis in Populus trichocarpa.  4CL catalyzes CoA ligation of many hydroxycinnamic acids, including 4-coumaric, caffeic, ferulic, 5-hydroxyferulic, and sinapic acids, into CoA thioesters for monolignol biosynthesis.  We have shown that a tight integration of in-vitro experimentation and computational modeling is capable of revealing unknown flux control mechanisms embedded in multi-enzyme reactions associated with Ptr4CL3, Ptr4CL5, and an identified Ptr4CL3/Ptr4CL5 complex. We generated a plausible hypothesis for enzyme interaction where 4CL5 is the main controlling factor.  Ptr4CL5 recruits Ptr4CL3 into the complex, causing any flux associated with free Ptr4CL3 to reduce to low amounts. This allows us to formulate hypotheses on the existence of nonlinear in-vivo control that extends beyond the linear regulation of gene expression. These results provide a key step towards creating a complete predictive model of lignin biosynthesis. (This work is supported by the National Science Foundation, Plant Genome Research Program grant, DBI-0922391, to VLC.)