EXPLOITING TALE (KNOX/BLH) TRANSCRIPTION FACTORS REGULATORY NETWORKS TO INCREASE CROP PRODUCTION

The Three Amino acid Loop Extension (TALE) proteins constitute an ancestral superclass of homeodomain transcription factors conserved in animals, plants and fungi, which play major roles in development. In plants they comprise two classes, KNOTTED1-LIKE homeobox (KNOX) and BEL1-like homeobox (BLH or BELL), which form heterodimers with different target affinity. KNOX and BLH genes are key players in morphogenetic processes at the shoot apical meristem (leaf, stem and inflorescence development, transition to flowering) and in legume root nodule organogenesis. TALE transcription factors cooperate to establish boundaries between undifferentiated cells and organ outgrowth through the modulation of multiple hormonal pathways, thus affecting several different plant developmental processes. Due to their pleiotropic effects, strategies to exploit TALE transcription factors potential for crop improvement need to: i) focus on fine tuning of gene expression of specific TALE TFs; ii) to selectively uncouple regulation of TALEs and their specific targets, the latter being mostly unknown. Also, very little is known about how specific KNOX and BLH homo- and heterodimers regulate subsets of target genes in different cells and developmental context. Based on previous knowledge of the developmental processes controlled by TALE transcription factors, we selected tissue-specific or developmental series transcript profiling data (obtained in our lab or publicly available) to construct TALE gene co-expression networks in model and crop species. Different algorithms, "a priori" functional module selection and extensive examination of network properties, like node degree distribution and gene centrality, were used to extract information on TALE gene regulatory networks. Such information was integrated with genome-wide in silico analyses of TALE binding sites to predict tissue/development-specific direct targets and design strategies to modify TALE regulatory networks to increase crop production.