Genome-wide Analysis Of Proteases And Inhibitors Sequences Identified Through Bioinformatics Data Mining In Four Tapeworms

Tapeworm belongs to Class Cestoda of Phylum Platyhelminthes. There are approximately5000specieson the earth, and among them, some species, such as Echinococcus granulosus, E. multilocularis,Taenia solium and so on, pose great threat to human and animal health. During living in livers, lungsand other organs of human and animals, metacestode larvae of E. granulosus and E. multilocularis leadto liver and/or lung hydatid disease. Neurocysticercosis or muscle cysticercosis occurs whenmetacestodes of T. solium are situated in the brain or muscle of human and animals. Prevention andtreatment on these parasitic diseases have important public health significance. Researches on novelefficient chemotherapeutic agents and immunoprophylaxis vaccines against parasites are emerging to behotspots in this field. It is a key step to screen and identify the chemotherapy targets and vaccinecandidates for the development of chemotherapeutic drugs and vaccines. Recently, the project ofsequencing and annotation of the genomes of T. solium, E. granulosus, E. multilocularis andHymenolepis microstoma has been completed. The data will provide rich resources for further studieson prevention and treatment methods against cestode infections.Proteases, also termed proteinases or peptidases, are proteolytic enzymes, involved in variousphysiological processes of all living organisms through regulating protein activation, synthesis andfolding of target proteins or molecules. Proteases are also essential for replication and dissemination ofviral, bacterial, parasitic and related pathogens, and therefore, the proteases are important targets forvaccines and drugs.In the present study, we identified and described the numbers, types, and potential functions of theproteases and their inhibitors from the putative proteomic data of four tapeworms using bioinformaticstechnology, combined with some databases. The results are as follows.1. After culling the data of redundant sequences, inactive homologs and putative pseudogenes, we haveidentified199,179,189and172proteases, which correspond to1.67%,1.75%,1.8%and1.70%of thepredicted proteins of T. solium （Asian strain）, E. granulosus, E. multilocularis and H. microstoma,respectively.2. As expected, the proteases identified here are grouped into five catalytic classes with differentproportions:2%-12%aspartic proteases,25%-29%cysteine proteases,33%-35%metalloproteases,20%-28%serine proteases, and7.5%-8.4%threonine proteases, respectively, in four tapeworms. These proportions are largely in harmony with those from other organisms. Among five classes, theproportions of the aspartic proteases in T. solium （12%） is greater than those in other three tapeworms（2.2%-3.7%）, and no significant differences are observed in other four protease classes among fourtapeworms. Comparatively, the proportions of the threonine proteases in the four tapeworms are higherthan those of Schistosoma mansoni （6%） and Caenorhabditis elegans （5%）. We also note that obviousexpansion in the relative proportion of the aspartic proteases in T. solium compared to S. mansoni （4%）and C. elegans （5%）. In the cysteine protease classes, a large number of Cathepsins and ubiquitinationand deubiquitination proteases were identified. Also, lots of trypsin-like proteases and subtilisin-likeserine endopeptidase were observed in the serine proteases.3. KAAS （KEGG Automatic Annotation Server） was able to assign orthology and KEGG （KyotoEncyclopedia of Genes and Genomes） functional pathways to117,163,146and165of T. solium, E.granulosus, E. multilocularis and H. microstoma proteases, respectively. Among them, the largestnumber of proteases is assigned to be engaged in human diseases:37,59,50and62in the fourtapeworms, respectively.24,20,20and27proteases are assigned to be involved in metabolic processes（including energy, nucleotide, amino acid and drug metabolism）, respectively, while19,22,22and19proteases are involved in genetic information processing, respectively.21,27,25and25are involved incellular processes （such as communication and cell cycling）, and8,10,9,13and8,25,20,19proteasesof the four tapeworms participate in environmental information processes and organismal systems,respectively. Comparatively, among the four tapeworms, a larger number of proteases are supposed tobe involved in human diseases in T. solium than those in other three cestodes.4. We identified35,38,36and27protease inhibitors from T. solium, E. granulosus, E. multilocularisand H. microstoma genomes, respectively, while inactive homologs and putative pseudogenes are notincluded. These inhibitors are classed into6-7inhibitor families, and most of them are containingN-terminal signal peptide sequence （44%-72%） and transmembrane α helix （15%-31%）.5. The protease inhibitors identified here consist of Kunitz serine protease inhibitors, serine proteaseinhibitors （serpins）, caspase inhibitors （BIR）, Cystatin （Cystatins） and so on. We observed that20,21,20and14proteins containing at least one Kunitz domains were present in the four cestodes genomes,respectively, and the majority of these Kunitz serine proteases contained a N-terminal signal peptidesequence. Almost all of these Kunitz domains were comprised of conserved three disulfide bonds.In addition, we identified5,6,4and6serine protease inhibitors （serpins） in these four tapeworms,which contain a conservative reactive center loop. It is noted that the serpins sequences of E.multilocularis （EmuJ₀01193100） identified here are the same as that of serpinEmureported by Merckelbach and Ruppel in2007.In conclusion, these comprehensive analyses on these proteases will not only represent a goodcomplement to the growing knowledge of proteolytic enzymes, but also provide a foundation forexpanding our knowledge in cestodes and exploring potential targets for the development of newchemotherapies and immunoprophylaxis...