Identification of cis-regulatory elements of TERMINAL FLOWER1 (TFL1) orthologues in Brassicaceae and Solanaceae plant families

Abstract

The TERMINAL FLOWER1 (TFL1) gene acts as an architect in flowering plants. By repressing floral transition in the shoot meristems where it is expressed, TFL1 regulates the life cycle of the plants, their growth pattern and the branching of the inflorescences. Although these functions have been well documented in the literature, the regulatory mechanisms remain largely unknown. In Arabidopsis thaliana, the expression of TFL1 in the shoot apical meristem maintains the inflorescence indeterminate (a raceme). Various cis-regulatory elements have been identified in the 5’- and 3’- regions of the TFL1 gene, and their distinct roles have been demonstrated by fusion with a reporter gene. The orthologue of TFL1 in Solanum lycopersicum (tomato) is the SELF-PRUNING (SP) gene, according to the literature. It does not affect the architecture of the inflorescence but represses the flowering of axillary buds, and so controls the sympodial growth habit of the plant. The aim of my master thesis is to identify cis-regulatory elements of TFL1-like genes to understand their different roles. The work starts with the construction of phylogenetic trees showing first the evolutionary history of the PEBP gene family to which TFL1 belongs, and then the history of the TFL1 orthologous genes in the plant families of Arabidopsis thaliana (Brassicaceae) and tomato (Solanaceae). The HMMER and Forty-Two methods were used to find the coding sequences of the TFL1-like genes in a set of Brassicaceae and Solanaceae genomes that I retrieved and verified manually. The phylogeny shows that the tomato gene that is closest to TFL1 is SP9D, while SP is closer to another gene in the TFL1 clade in Arabidopsis, ARABIDOPSIS THALIANA CENTRORADIALIS (ATC). The 5’ (0.5 kb) and 3’ (4 kb) regions as well as the intronic regions were extracted and phylogenetic trees were constructed for each of them. The use of various tools from the MEME SUITE then allowed to discover conserved motifs in the 5’- and 3’- regions of the genes in both plant families and to compare them. A verification was conducted by searching for the LEAFY (LFY) protein binding motif in the 3’- region of the sequences from the dataset of the TFL1 gene. For the four genes studied, the motifs shared in the -0.25 kb 5’- region are extremely conserved. For the 3’- region of the SP9D gene, MEME shows a strong difference between the motifs found in the Solanum genus and those present in the Nicotiana genus. The results obtained by the STREME tool are encouraging; they reveal motifs that are shared by more than 90% of the Solanaceae species, but are completely absent from the homologous sequences of the Brassicaceae family, both for the 3’- and 5’- regions. Some of these motifs correspond to motifs that are already known in databases (Tomtom tool). The next step will be to correlate these results with morphological or physiological traits to determine their potential regulatory role in plant architecture and life cycle diversity.