Bioinformatic characterization of aspartic protease (AP) enzyme in seed plants

Abstract

Aspartic proteases (APs; EC: 3.4.23) are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. They have been extensively studied and are widely distributed among vertebrates, plants, yeast, nematodes, parasites, fungi, and viruses. In this study, bioinformatic analyses of AP enzyme were performed in seed plants protein sequences, including 33 species of 14 different families. According to the conserved motifs obtained by MEME and MAST tools, two motifs were common in all seed plants. The structural and functional analyses of six selected monocots and dicots were investigated by ProtParam, SOPMA, SignalP 4.1, TMHMM 2.0 and ProDom tools in ExPASy database. Tertiary structure of Arabidopsis thaliana as a sample of seed plants, was predicted by Phyre2 server using “d1oewa” model (PDB accession code: 1oew) and its quality was verified by PROCHECK and ProSA-web servers. The protein sequences were aligned with ClustalW algorithm by MEGA 6.06 software and phylogenetic tree was constructed using the Neighbor-joining (NJ) method. In protein–protein interactions analysis by STRING 9.1 tool, 12 and 135 significant protein interaction groups were identified in Arabidopsis thaliana and other species, respectively. According to the results, there is a high identity among APs of different species in seed plants, so that they should be derived from a common ancestor. The approaches and results reported here would be useful to prioritize candidate genes for further functional proteomic studies of this enzyme in seed plants.