Systems Biology Models for Wall Biosynthesis Pathways.

Senior Personnel - Debra Mohnen (CCRC), Ed Uberbacher (ORNL), Ying Xu (UGA), Phuongan Dam (UGA), Maor Bar-Peled (CCRC).

Few of the genes required for cell wall biosynthesis have been functionally identified and many of the genes in current databases are incorrectly annotated or not annotated at all.

We will populate an expert-based database with known and putative cell wall-related genes using data management and modeling tools developed by BESC members (ORNL and UGA). This database will be continuously updated as new data are generated within BESC.

We will develop a computer-based information system (see Figure 1) that will allow us to rationally select genes whose modified expression leads to reduced recalcitrance.

Data incorporated into this information system will include:

          Genes that are activated or suppressed during maturation of tissues

          The function of these genes

          How their expression is controlled

          The types of tissue that synthesize specific cell wall polysaccharides

          The types of precursors that are made by these tissues

          How easily the cell walls of these tissues are deconstructed

The information system will allow us to draw correlations between recalcitrance, cell wall chemistry, and gene expression and to develop cell wall biosynthesis pathways and networks for use in identifying genes with potential roles in cell wall recalcitrance.

The expression of genes of potential interest will be modified in Populus and switchgrass.

Transformed plants will be subjected to the full battery of analytical tools available to BESC (e.g. expression profiling, function, expression, comparative genomic, QTL, bioinformatic, biochemical, chemical, and immunohistochemical analyses) to establish the effect of the gene on reducing recalcitrance.

We will use this data to develop high level systems biology models that in the long term will allow us to generate mechanistic hypotheses relating gene expression and recalcitrance.

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