Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis

The presence of lignin in secondary cell walls (SON) is a major factor preventing hydrolytic enzymes from gaining access to cellulose, thereby limiting the saccharification potential of plant biomass. To understand how lignification is regulated is a prerequisite for selecting plant biomass better adapted to bioethanol production. Because transcriptional regulation is a major mechanism controlling the expression of genes involved in lignin biosynthesis, our aim was to identify novel transcription factors (TFs) dictating lignin profiles in the model plant Arabidopsis. To this end, we have developed a post-genomic approach by combining four independent in-house SCVV-related transcriptome datasets obtained from (1) the fiber cell wall-deficient wati Arabidopsis mutant, (2) Arabidopsis lines over-expressing either the master regulatory activator EgMYB2 or (3) the repressor EgMYB1 and finally (4) Arabidopsis orthologs of Eucalyptus xylem-expressed genes. This allowed us to identify 502 up- or down regulated TFs. We preferentially selected those present in more than one dataset and further analyzed their in silico expression patterns as an additional selection criteria. This selection process led to 80 candidates. Notably, 16 of them were already proven to regulate SCVV formation, thereby validating the overall strategy. Then, we phenotyped 43 corresponding mutant lines focusing on histological observations of xylem and interfascicular fibers. This phenotypic screen revealed six mutant lines exhibiting altered lignification patterns. Two of them [Bel-like HomeoBox6 (b1176) and a zinc finger TF] presented hypolignified SCVV. Three others (rnyb52, rnyb-like TE ith5) showed hyperlignified SCW whereas the last one (hb15) showed ectopic lignification. In addition, our meta analyses highlighted a reservoir of new potential regulators adding to the gene network regulating SCVV but also opening new avenues to ultimately improve SCVV composition for biofuel production.