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.

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

“…Several other significantly enriched GOs are associated with this gene family. Cysteine proteases have been identified as major functional components of Venus flytrap (Dionaea muscipula) digestive fluid (72), reported in three D. muscipula transcriptomes (70,73,74), and structurally annotated for both Cape sundew (Drosera capensis) draft genome sequences (75,76) and D. muscipula (77). We found tandem clusters of homologous proteaseencoding genes in the U. gibba genome that had demonstrably undergone tandem duplication both before and after the most recent WGD event in U. gibba's evolutionary history (Fig.…”

Discovery of digestive enzymes in carnivorous plants with focus on proteases

“…have reported usage for dressing wounds and as a remedy for urinary infections and cough (Patel, 2014). To date, Genlisea aurea (Leushkin et al, 2013) and Utricularia gibba (Lan et al, 2017) are among the four carnivorous plants with genome sequences publicly available, apart from Drosera capensis (Butts, Bierma & Martin, 2016) and Cephalotus follicularis (Fukushima et al, 2017). The availability of genome sequences has contributed greatly to enzyme discovery and improving our understanding of carnivory mechanisms and evolution in different carnivorous plant families.…”

The Evolution Force of Genome Reduction in Carnivorous Plants

“…They often feed on microscopic and perform digestive functions in closed traps. Thus, they are less vulnerable to the environmental constraints in exposed environments (Butts et al, 2016). The genome sequencing results showed that the genome size difference between G. aurea and U. gibba was more than one time, 43 Mb vs 101 Mb.…”