TreeBASE Search-Matrices for study 15682

@ARTICLE{TreeBASE2Ref23106, author = {Hong-Bin Yan and Zhong-Zi Lou and Li Li and Paul J Brindley and Yadong Zheng and Xuenong Luo and Junling Hou and Aijiang Guo and Wan-Zhong Jia and Xuepeng Cai}, title = {Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium}, year = {2014}, keywords = {Proteases; Taenia solium; Drug target; Vaccine candidate antigen; Genome-wide analysis; Cysticercosis; Platyhelminth}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Genomics}, volume = {}, number = {}, pages = {}, abstract = {Background: Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere where pigs are farmed in close proximity to people and where sanitation processes are not optimal. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. Parasitologists have long focused their investigation on proteases, not only for the fundamental biochemical aspects of these enzymes but also because proteases represent potentially targetable checkpoints in the pathogens? physiology. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets. Results: Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases. Conclusion: Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis of tapeworm proteases not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from wihch to expand knowledge of cestode proteases and to explore their biochemistry and their potential as intervention targets. } }