Molecular dynamics and evolutionary conservation of FUL-SOC1 regulatory interactions in polyploid Brassica juncea.

Binding of FUL with SOC1 promoter is necessary for promoting floral transition. Structural insights on mechanisms of binding can be exploited to modify DNA–protein interactions. In polyploid Brassicas, naturally diverse homologs of FUL proteins and SOC1 promoters likely regulate flowering time by way of complex interactions patterns. The dynamics of these, however, remain unexplored. Herein, we report natural structural variation among 51 FUL homologs from 25 Brassicaceae species and 3 BjuSOC1promoter homeologs. The 5’-distal deletions of BjuSOC1promoters with diverse TFBS profiles, exhibited differential GUS activity. Genetic complementation of soc1-2 mutant with BjupSOC1: AtSOC1 constructs revealed differential strength of promoter homeologs, manifesting as variable potential of flowering and AtSOC1 levels. Despite structural variation, docked FUL:pSOC1 complexes, depicted similar binding affinity stabilized by both conserved and unique residues. Molecular dynamics simulations highlighted impact of mutations on interactions. Root Mean Square Deviation revealed conformational flexibility of docked FUL: pSOC1 complexes, while Root Mean Square Fluctuation values demonstrated structural flexibility of FUL proteins bound to SOC1 promoters. The MM-GBSA-based binding free energy parameters and interaction mapping showed that mutations in FUL proteins and SOC1 promoters are compensatory permitting conservation of interaction potential. Yeast one-hybrid assays validated in silico interaction patterns. This study is essential since interacting amino-acid and nucleotide residues can be modified to design novel alleles of FUL and SOC1 with enhanced binding potential to achieve early flowering, a key agronomic trait.