Lignin is an aromatic heteropolymer that is mainly deposited in the walls of secondary-thickened cells. It makes up 20-30% of the dry weight of wood. In dicotyledonous plants, lignin is biosynthesized mainly by the combinatorial coupling of coniferyl and sinapyl alcohol (Boerjan et al., 2003).

Although the roles of most of the monolignol pathway genes in determining lignin amount and composition have been elucidated, knowledge on how monolignol biosynthesis integrates into wider plant metabolism, and how plant metabolism responds to changes in the expression of individual monolignol biosynthesis genes, is still scarce. Using transcriptome and metabolome-wide analyses, such interactions can now be revealed. Indeed, deep phenotyping of transgenic plants with defects in monolignol biosynthesis reveals far-reaching consequences on gene expression in various pathways (Rohde et al., 2003; Dauwe et al., 2007; Leplé et al., 2007). Knowledge of these broader effects at the transcriptome and metabolome level is essential if we want to fully comprehend the relationships between gene function and cell wall properties, how these cell wall properties are elaborated, and how they relate to the quality of raw material destined for agro-industrial processes (Vanholme et al., 2010). This knowledge will also shed light on the molecular pathways involved in possible negative side effects of lignin engineering, information that will be needed to mitigate these effects by pathway engineering.

To achieve this goal, we have identified all genes in the Arabidopsis genome that share homology with known genes in monolignol biosynthesis (Raes et al., 2003) and have characterized the corresponding mutants by combined microarray, metabolome (LC/MS, GC/MS and FTMS) and computational analysis. The function of selected genes ensuing from the computational analyses is studied by reverse genetics in Arabidopsis. For genes with potential agricultural value, transformation of poplar and corn is envisaged as proof of concept.