title: 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.
authors.affiliation: Department of Electrical Engineering and Computer Science, UC Irvine, Irvine, California, 92697. rwmartin@uci.edu.|Department of Statistics, UC Irvine, Irvine, California, 92697. rwmartin@uci.edu.|Department of Sociology, UC Irvine, Irvine, California, 92697. rwmartin@uci.edu.
authors.forename: Carter T
authors.initials: CT
authors.lastname: Butts
authors.affiliation: Department of Molecular Biology and Biochemistry, UC Irvine, Irvine, California, 92697.
authors.forename: Jan C
authors.initials: JC
authors.lastname: Bierma
authors.affiliation: Department of Molecular Biology and Biochemistry, UC Irvine, Irvine, California, 92697. buttsc@uci.edu.|Department of Chemistry, UC Irvine, Irvine, California, 92697. buttsc@uci.edu.
authors.forename: Rachel W
authors.initials: RW
authors.lastname: Martin
mesh_terms: D000595:Amino Acid Sequence; D060435:Carnivory / Q000502:physiology*; D020134:Catalytic Domain; D020451:Contig Mapping; D029787:Drosera / Q000145:classification / Q000235:genetics*; D031257:Droseraceae / Q000145:classification / Q000235:genetics*; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D062105:Molecular Docking Simulation; D058977:Molecular Sequence Annotation; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000072417:Protein Domains; D017510:Protein Folding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D013379:Substrate Specificity
chemical_list: D010940:Plant Proteins; D010447:Peptide Hydrolases
keywords: Rosetta; aspartic protease; carnivorous plant; cysteine protease; digestive enzyme; enzyme substrate specificity; genome sequence; molecular docking; plant-specific insert; protein structure prediction