Identification of amino acids involved in homo and hetero dimerization of MtKNOX3 transcription factor during nodule development in Medicago truncatula: An In-silico study

KNOX family of transcription factors plays an important role in plant growth and development. These transcription factors are involved in maintaining the undifferentiated state of meristem cells in shoot apical meristem. The transcription factor KNOX3 is expressed during the development of nitrogen fixation nodules in Medicago truncatula and it has been shown that it can affect the expression of cytokinin biosynthesis genes. Proteins of KNOX family often act through homo- or heterodimerization with BELL transcription factors. Recent studies showed that the transcription factor MtBELL1-2 has high expression level during nodule development in M. truncatula and this transcription factor can interact with MtKNOX3. The aim of this study is to identify the binding sites in MtKNOX3-MtKNOX3 homodimer and MtKNOX3-MtBELL1-2 heterodimer. To identify the binding sites, various bioinformatics methods was used including methods based on protein sequence, the relative accessible areas of proteins, docking methods, alanine scanning, and identification of conserved amino acids. According to the obtained results, the MEINOX domain and the homeodomain are involved in the interaction of MtKNOX3-MtBELL1-2 heterodimer, which is consistent with the previous data regarding the interaction of their homologous proteins in Arabidopsis. Regarding the MtKNOX3-MtKNOX3 homodimer, in addition to the mentioned domains, an area upstream of the MEINOX domain is also important.