Abstract
Carnivorous plants represent a so far underexploited reservoir of novel proteases with potentially useful activities. Here we investigate 44 cysteine proteases from the Cape sundew, Drosera capensis, predicted from genomic DNA sequences. D. capensis has a large number of cysteine protease genes; analysis of their sequences reveals homologs of known plant proteases, some of which are predicted to have novel properties. Many functionally significant sequence and structural features are observed, including targeting signals and occluding loops. Several of the proteases contain a new type of granulin domain. Although active site residues are conserved, the sequence identity of these proteases to known proteins is moderate to low; therefore, comparative modeling with all-atom refinement and subsequent atomistic MD-simulation is used to predict their 3D structures. The structure prediction data, as well as analysis of protein structure networks, suggest multifarious variations on the papain-like cysteine protease structural theme. This in silico methodology provides a general framework for investigating a large pool of sequences that are potentially useful for biotechnology applications, enabling informed choices about which proteins to investigate in the laboratory.
Highlights
The proteases of carnivorous plants present attractive targets for exploitation in chemical biology and biotechnology contexts
Given that plant carnivory appears to have evolved from defensive systems in general [16], and that the feeding responses are triggered by the same signaling pathway as is implicated in response to wounding [17], one would expect cysteine proteases to play a major role; here we investigate some of the many cysteine protease genes in D. capensis with the objective of adding to the portfolio of cleavage activities available for chemical biology applications
All D. capensis sequences previously annotated as coding for MEROPS C1 cysteine proteases using the MAKER-P (v2.31.8) pipeline [39] and a BLAST search against SwissProt and InterProScan [40] were clustered by sequence similarity
Summary
The proteases of carnivorous plants present attractive targets for exploitation in chemical biology and biotechnology contexts Carnivorous plants, such as Drosera capensis, whose prey capture functions take place in the open have been rigorously selected by evolution for the ability to digest large prey over long time periods, without assistance from physical disruption of prey tissue, and in competition with ubiquitous fungi and bacteria. These evolutionary constraints have selected for highly stable enzymes with a different profile of substate specificities and cleavage patterns from those found in animal digestive enzymes.
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