Transcriptional regulators of Arabidopsis secondary cell wall formation: tools to re-program and improve cell wall traits

Secondary cell walls (SCWs) comprise the main portion of plant biomass and represent an abundant renewable resource of polysaccharides for conversion into sugars and subsequent fermentation to liquid biofuels. An upswing in lignocellulosic biomass-derived biofuels, including from grass and woody energy crops and agricultural residues, offers significant environmental and socio-economic benefits over the use of dwindling and polluting non-renewable fossil fuels. A key challenge for realizing commercial biofuel production resides in the economically unfeasible sugar yields after enzymatic hydrolysis of lignocellulosic biomass. This low saccharification efficiency is caused by the recalcitrant nature of the cell wall owing to the crystallinity of cellulose and interactions between the polysaccharides and lignin polymers within the cell wall matrix (Himmel et al., 2007; Demartini et al., 2013). Overcoming biomass recalcitrance has generally been tackled with costly and energy intensive pre-treatments, which so far have met bioconversion requirements with limited success. One alternative path to optimize the digestibility of lignocellulose for sustainable biofuel production is the genetic manipulation of SCW characteristics via transcription factors (TFs), powerful tools to orchestrate the biosynthesis and deposition of the main SCW components cellulose, lignin, and hemicellulose. Research efforts have revealed an extensive, complex and hierarchical regulatory network of SCW-related TFs predominantly comprising NAC and MYB family members in Arabidopsis (Handakumbura and Hazen, 2012; Hussey et al., 2013). Delineating the topology and dynamics of this regulatory network will require exploring its nodes, hubs, and edges. Cassan-Wang et al. (2013) confront these fundamental goals by tallying new TFs to the network regulating SCW formation in Arabidopsis. Their innovative strategy to identify transcriptional regulators involved the exploitation of several Arabidopsis SCW-related transcriptome datasets combined with in silico expression and histology-based phenotyping screens. Since lignin is commonly acknowledged to inhibit biomass digestibility, their systematic approach proved useful as six TDNA lines from candidate TFs revealed altered lignin deposition profiles; including hyperand hypo-lignification as well as ectopic lignin deposition (Cassan-Wang et al., 2013). Co-expression analysis suggests that some of these TFs not only play a role in lignin biosynthesis, but also regulate other parts of the SCW formation program including cellulose and xylan biosynthesis. It is noteworthy that the majority of T-DNA/RNAi lines corresponding to candidate SCW-related TFs did not reveal a lignin phenotype. The fact that their candidate list of TFs contains known SCW regulators validates the robustness of their identification strategy. However, it is well established that redundancy exists among TFs and the authors, therefore, rightly touch upon the need for analyzing over-expressor lines and/or multiple gene knock-out mutants of homologous TFs in order to increase the likelihood of a detectable SCW phenotype and understanding of gene function. One approach that has been particularly successful in addressing this problem of functional redundancy is that of dominant repression (Hiratsu et al., 2003). The expression of chimeric repressors (specific TF fused to a repression domain) induces loss-of-function phenotypes in transgenic plants by dominating the activity of both endogenous and functionally redundant TFs, facilitating the analysis of TF function in SCW formation (Zhong et al., 2007; McCarthy et al., 2009). The identification of the lignin mutants by Cassan-Wang et al. (2013) was ultimately based on histological observations and more extensive compositional analysis might increase the number of SCW-related mutants beyond the six already identified. For instance, it is known that certain SCW-related TFs regulate specific lignin monomers (Zhao et al., 2010; Öhman et al., 2013). The ratios of these monomers may therefore have been shifted in some TF mutants, without causing an obvious phenotype for plant growth or lignin staining but potentially affecting recalcitrance and saccharification yield.