Identification of Regulators in Grass Secondary Cell Wall Biosynthesis Via Gene Network Analysis in Rice

Cell wall deconstruction inefficiency is a key problem for biofuel production from cellulosic biomass. Relatively few studies have examined SCW regulators in grasses, which may have diverged from dicots in terms of regulatory mechanisms, as they have in cell wall composition and patterning. To identify new genes controlling grass SCW biosynthesis, we used three publicly available rice gene association networks, ROAD, PlaNet and RiceNet, and various combinations of them. From these networks, we extracted SCW subnetworks around homologs of known cell wall-related transcription factors, lignin biosynthesis genes, and putative grass-diverged crosslinking enzymes. Of the various networks, the SCW subnetwork built using a general linear model (GLM) to combine the three networks showed the largest biological pathway Gene Ontology-term match ratio, indicating high network quality. The GLM-network is also enriched with non-bait cell wall metabolic terms. So far, we have tested eight protein-promoter interactions predicted in the GLM-subnetwork between transcription factors and SCW biosynthesis pathway genes with a luciferase transient assay. Four of interactions are novel. Of these, six of them show increased luciferase production in the presence of the transcription factor relative to its absence. Genetic analysis of the roles of some of the validated transcription factors is now underway. This analysis provides evidence for the function of previously unstudied transcription factors in grass cell wall regulation. Furthermore, it facilitates transfer of understanding of regulatory mechanisms among species to enable control of SCW biosynthesis in grasses for improved fuel, feed, and fiber production.