Haplotype analysis, regulatory elements and docking simulation of structural models of different AT3 copies in the genus .

Capsaicinoids are responsible for the pungency in species. These are synthesized by the Capsaicin synthase (CS) encoded by the gene, which catalyzes the transference of an acyl moiety from a branched-chain fatty acid-CoA ester to the vanillylamine to produce capsaicinoids. Some gene copies have been identified on the genome. The absence of capsaicinoid in some nonpungent accessions is related to mutant alleles. The differences between CS protein copies can affect the tridimensional structure of the protein and the affinity for its substrates, and this could affect fruit pungency. This study characterized 32 AT3 sequences covering pungent and non-pungent accessions. These were clustered in AT3-D1 and AT3-D2 groups and representative sequences were analyzed. Genomic upstream analysis shows different regulatory elements, mainly responsive to light and abiotic stress. and gene expression was confirmed in fruit tissues of . Amino acid substitutions close to the predictable HXXXD and DFGWG motifs were also identified. sequences were modeled showing a BAHD acyltransferase structure with two connected domains. A pocket with different shape, size and composition between AT3 models was found inside the protein, with the conserved motif HXXXD exposed to it, and a channel for their accessibility. CS substrates exhibit high interaction energies with the His and Asp conserved residues. AT3 models have different interaction affinities with the (E)-8-methylnon-6-enoyl-CoA, 8-methylnonanoyl-CoA and vanillylamine substrates. These results suggested that AT3-D1 and AT3-D2 sequences encode CS enzymes with different regulatory factors and substratum affinities.Communicated by Ramaswamy H. Sarma.