Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis

ABSTRACT In his 1875 monograph on insectivorous plants, Darwin described the feeding reactions of Drosera flypaper traps and predicted that their secretions contained a “ferment” similar to mammalian pepsin, an aspartic protease. Here we report a high‐quality draft genome sequence for the cape sundew, Drosera capensis , the first genome of a carnivorous plant from order Caryophyllales, which also includes the Venus flytrap ( Dionaea ) and the tropical pitcher plants ( Nepenthes ). This species was selected in part for its hardiness and ease of cultivation, making it an excellent model organism for further investigations of plant carnivory. Analysis of predicted protein sequences yields genes encoding proteases homologous to those found in other plants, some of which display sequence and structural features that suggest novel functionalities. Because the sequence similarity to proteins of known structure is in most cases too low for traditional homology modeling, 3D structures of representative proteases are predicted using comparative modeling with all‐atom refinement. Although the overall folds and active residues for these proteins are conserved, we find structural and sequence differences consistent with a diversity of substrate recognition patterns. Finally, we predict differences in substrate specificities using in silico experiments, providing targets for structure/function studies of novel enzymes with biological and technological significance. Proteins 2016; 84:1517–1533. © 2016 Wiley Periodicals, Inc.