Ron Sederoff

Plant cell walls are the essential components of feedstocks for biomass based liquid fuel alternatives to petroleum. The secondary cell walls of woody plants contribute greatly to biomass and are targets for improving potential feedstocks. In the application of systems biology to development of new biofuels, as in any complex biological process, predictive modeling is the central goal. We propose to use a systems approach with genome based information and mathematical modeling to advance the understanding of the biosynthesis of the plant secondary cell wall. To do this, we will use multiple transgenic perturbations and measure effects on plants using advanced quantitative methods of genomics, proteomics, and structural chemistry. The combination of quantitative analysis, transgenesis, statistical inference and systems modeling provide a novel and comprehensive strategy to investigate the regulation, biosynthesis and properties of the secondary cell wall.

Lignin is a unique and complex phenylpropanoid polymer, important in plant development and response to environment. We propose to advance our knowledge of lignin biosynthesis by developing a comprehensive pathway model of regulatory and metabolic flux control mechanisms. Our primary tool will be systematic gene specific perturbation in transgenic Populus trichocarpa. We will perturb all 34 known lignin pathway and regulatory network genes in P. trichocarpa using artificial microRNA (amiRNA) and RNAi suppression. From each independent transgenic perturbation, we will obtain quantitative information on transcript and protein abundance, enzyme kinetics, metabolite concentrations, and lignin structural chemistry. Using statistical correlation and path analysis, we will integrate this information to develop a mechanistic-based signaling graph and metabolic flux model for the pathway and its regulation leading to specific lignin structures. This model will reveal regulatory constraints on steady-state flux distributions and show how genes and other process components affect flux activity of lignin precursors, composition, and linkages. In this way, we will provide a systems biology approach to this fundamental pathway. There are few opportunities in higher plants to integrate genomics, biochemistry, chemistry and modeling to develop a comprehensive understanding of biosynthesis and structure of a major component of morphology and adaptation.

Angiosperm species, such as Eucalyptus globulus, have lignin composed of both syringyl and guaiacyl subunits. In contrast, gymnosperm species such as Pinus taeda have lignin which is devoid of syringyl monomer units. Favorable pulping efficiency with high pulp yields has long been associated to wood with lignin containing high syringyl component. Inducing the biosynthesis of syringyl subunits in gymnosperm lignin would be a direct approach to engineer gymnosperm wood for improved pulping efficiency and yields. Here, we propose to establish a strategy to demonstrate the induction of syringyl monolignol biosynthesis in gymnosperms through an in vitro protein activity assay system. In this system, we plan to spike the total protein mixtures isolated from the secondary differentiating xylem (SDX) of a gymnosperm with angiosperm syringyl-lignin specific recombinant proteins. We will assay these protein mixtures using coniferaldehyde, a common precursor to both guaiacyl and syringyl monolignols, and monitor the synthesis of sinapyl and coniferyl alcohol, precursors of syringyl and guaiacyl monolignol respectively. These assays will provide insights to the extent of syringyl monolignol biosynthesis we can induce into gymnosperms by the addition of angiosperm proteins.

WHEREAS, the parties to this Agreement intend to join together in a cooperative effort to support a FOREST BIOTECHNOLOGY INDUSTRIAL RESEARCH CONSORTIUM (hereinafter called ?CONSORTIUM?) at UNIVERSITY to develop a better understanding of fundamental information about the growth and development of trees, to promote innovative research for improved trees with desired properties using the most advanced forest biotechnology, to foster interactions between industry and university researchers, and to facilitate further research cooperation between the parties.

Whereas, the parties to this Agreement intend to join together in a cooperative effort to support a FOREST BIOTECHNOLOGY INDUSTRIAL RESEARCH CONSORTIUM (hereinafter called "CONSORTIUM") at UNIVERSITY to develop a better understanding of fundamental information about the growth and development of trees, to promote innovative research for improved trees with desired properties using the most advanced forest biotechnology, to foster interactions between industry and university researchers, and to facilitate further research cooperation between the parties.