Expression Profile of the Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets

Blood fluke proteases play pivotal roles in the processes of invasion, nutrition acquisition, immune evasion, and other host-parasite interactions. Hundreds of genes encoding putative proteases have been identified in the recently published schistosome genomes. However, the expression profiles of these proteases in Schistosoma species have not yet been systematically analyzed. We retrieved and culled the redundant protease sequences of Schistosoma japonicum, Schistosoma mansoni, Echinococcus multilocularis, and Clonorchis sinensis from public databases utilizing bioinformatic approaches. The degradomes of the four parasitic organisms and Homo sapiens were then comparatively analyzed. A total of 262 S. japonicum protease sequences were obtained and the expression profiles generated using whole-genome microarray. Four main clusters of protease genes with different expression patterns were identified: proteases up-regulated in hepatic schistosomula and adult worms, egg-specific or predominantly expressed proteases, cercaria-specific or predominantly expressed proteases, and constantly expressed proteases. A subset of protease genes with different expression patterns were further validated using real-time quantitative PCR. The present study represents the most comprehensive analysis of a degradome in Schistosoma species to date. These results provide a firm foundation for future research on the specific function(s) of individual proteases and may help to refine anti-proteolytic strategies in blood flukes.

[1]  Jindrich Fanfrlík,et al.  Structural Basis for Inhibition of Cathepsin B Drug Target from the Human Blood Fluke, Schistosoma mansoni* , 2011, The Journal of Biological Chemistry.

[2]  Elaine R. Mardis,et al.  The draft genome of the parasitic nematode Trichinella spiralis , 2011, Nature Genetics.

[3]  Sheila Donnelly,et al.  Helminth pathogen cathepsin proteases: it's a family affair. , 2008, Trends in biochemical sciences.

[4]  P. Loke,et al.  Proteases in parasitic diseases. , 2006, Annual review of pathology.

[5]  Jürg Utzinger,et al.  Praziquantel: mechanisms of action, resistance and new derivatives for schistosomiasis , 2008, Current opinion in infectious diseases.

[6]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[7]  Patricia C. Babbitt,et al.  SmCL3, a Gastrodermal Cysteine Protease of the Human Blood Fluke Schistosoma mansoni , 2009, PLoS neglected tropical diseases.

[8]  X. Deng,et al.  The COP9 signalosome: more than a protease. , 2008, Trends in biochemical sciences.

[9]  David Rollinson,et al.  Schistosome genomes: a wealth of information. , 2010, Trends in parasitology.

[10]  Joyce To,et al.  Collagenolytic Activities of the Major Secreted Cathepsin L Peptidases Involved in the Virulence of the Helminth Pathogen, Fasciola hepatica , 2011, PLoS neglected tropical diseases.

[11]  Sandra D. Melman,et al.  Reduced Susceptibility to Praziquantel among Naturally Occurring Kenyan Isolates of Schistosoma mansoni , 2009, PLoS neglected tropical diseases.

[12]  M. Sajid,et al.  Blood 'n' guts: an update on schistosome digestive peptidases. , 2004, Trends in parasitology.

[13]  Pengfei Cai,et al.  Genome-wide identification and characterization of a panel of house-keeping genes in Schistosoma japonicum. , 2012, Molecular and biochemical parasitology.

[14]  J. Vondrášek,et al.  Mapping the pro-peptide of the Schistosoma mansoni cathepsin B1 drug target: modulation of inhibition by heparin and design of mimetic inhibitors. , 2011, ACS chemical biology.

[15]  M. Sajid,et al.  A Blood Fluke Serine Protease Inhibitor Regulates an Endogenous Larval Elastase* , 2011, The Journal of Biological Chemistry.

[16]  Gail M Williams,et al.  Schistosomiasis elimination: lessons from the past guide the future. , 2010, The Lancet. Infectious diseases.

[17]  Andreas Ruppel,et al.  Invasion by schistosome cercariae: neglected aspects in Schistosoma japonicum. , 2004, Trends in parasitology.

[18]  Robert N. Pike,et al.  Vector-based RNA interference of cathepsin B1 in Schistosoma mansoni , 2010, Cellular and Molecular Life Sciences.

[19]  K. C. Lim,et al.  Proteomic Analysis of Human Skin Treated with Larval Schistosome Peptidases Reveals Distinct Invasion Strategies among Species of Blood Flukes , 2011, PLoS neglected tropical diseases.

[20]  Gonzalo R. Ordóñez,et al.  The Degradome database: mammalian proteases and diseases of proteolysis , 2008, Nucleic Acids Res..

[21]  Neil D. Rawlings,et al.  MEROPS: the database of proteolytic enzymes, their substrates and inhibitors , 2013, Nucleic Acids Res..

[22]  Denis M Larkin,et al.  Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery. , 2011, Trends in parasitology.

[23]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[24]  J. Dalton,et al.  A method for the isolation of schistosome eggs and miracidia free of contaminating host tissues , 1997, Parasitology.

[25]  Ben Herbert,et al.  Proteomics and Phylogenetic Analysis of the Cathepsin L Protease Family of the Helminth Pathogen Fasciola hepatica , 2008, Molecular & Cellular Proteomics.

[26]  Matthew Bogyo,et al.  Hemoglobin digestion in blood-feeding ticks: mapping a multipeptidase pathway by functional proteomics. , 2009, Chemistry & biology.

[27]  Satoru Miyano,et al.  Open source clustering software , 2004 .

[28]  C. Caffrey,et al.  Chemotherapy of schistosomiasis: present and future. , 2007, Current opinion in chemical biology.

[29]  Minoru Nakao,et al.  Cloning and characterization of cathepsin L-like peptidases of Echinococcus multilocularis metacestodes. , 2007, Molecular and biochemical parasitology.

[30]  M. Bogyo,et al.  New approaches for dissecting protease functions to improve probe development and drug discovery , 2012, Nature Structural &Molecular Biology.

[31]  Jennifer Y. King,et al.  Pathway analysis of coronary atherosclerosis. , 2005, Physiological genomics.

[32]  Carolina Piña-Vázquez,et al.  Host-Parasite Interaction: Parasite-Derived and -Induced Proteases That Degrade Human Extracellular Matrix , 2012, Journal of parasitology research.

[33]  Jan Dvorák,et al.  Differential use of protease families for invasion by schistosome cercariae. , 2008, Biochimie.

[34]  Yan Huang,et al.  The draft genome of the carcinogenic human liver fluke Clonorchis sinensis , 2011, Genome Biology.

[35]  Hirohisa Hirai,et al.  Schistosome egg production is dependent upon the activities of two developmentally regulated tyrosinases , 2007, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[36]  A. Da'dara,et al.  Suppression of cathepsin B expression in Schistosoma mansoni by RNA interference. , 2003, International journal for parasitology.

[37]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[38]  Wei Huang,et al.  The Schistosoma japonicum genome reveals features of host–parasite interplay , 2009, Nature.

[39]  Jan Dvorák,et al.  A Multienzyme Network Functions in Intestinal Protein Digestion by a Platyhelminth Parasite* , 2006, Journal of Biological Chemistry.

[40]  Adam R Renslo,et al.  Drug discovery and development for neglected parasitic diseases , 2006, Nature chemical biology.

[41]  B. Turk.  Targeting proteases: successes, failures and future prospects , 2006, Nature Reviews Drug Discovery.

[42]  Jian Wang,et al.  Whole-genome sequence of Schistosoma haematobium , 2012, Nature Genetics.

[43]  Jan Dvorák,et al.  Aza-peptidyl Michael acceptor and epoxide inhibitors--potent and selective inhibitors of Schistosoma mansoni and Ixodes ricinus legumains (asparaginyl endopeptidases). , 2009, Journal of medicinal chemistry.

[44]  David S. Roos,et al.  Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach , 2010, PLoS neglected tropical diseases.

[45]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[46]  D. Begun,et al.  Molecular population genetics of female-expressed mating-induced serine proteases in Drosophila melanogaster. , 2007, Molecular biology and evolution.

[47]  Jacqueline A. Keane,et al.  The genomes of four tapeworm species reveal adaptations to parasitism , 2013, Nature.

[48]  Andreas Ruppel,et al.  SmCB2, a novel tegumental cathepsin B from adult Schistosoma mansoni. , 2002, Molecular and biochemical parasitology.

[49]  Jing Xu,et al.  Molecular cloning and analysis of stage and tissue-specific expression of Cathepsin L-like protease from Clonorchis sinensis , 2009, Parasitology Research.

[50]  Anna V. Protasio,et al.  Trypsin- and Chymotrypsin-Like Serine Proteases in Schistosoma mansoni – ‘The Undiscovered Country’ , 2014, PLoS neglected tropical diseases.

[51]  Dennis J Minchella,et al.  Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome , 2009, BMC Genomics.

[52]  R. Desnick,et al.  Cholesteryl ester storage disease: review of the findings in 135 reported patients with an underdiagnosed disease. , 2013, Journal of hepatology.

[53]  Akiyasu C. Yoshizawa,et al.  KAAS: an automatic genome annotation and pathway reconstruction server , 2007, Environmental health perspectives.

[54]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[55]  Luc Kestens,et al.  Human schistosomiasis , 2006, The Lancet.

[56]  Michele Cavo,et al.  Proteasome inhibitors in multiple myeloma: 10 years later. , 2012, Blood.

[57]  Petr Horák,et al.  The functional expression and characterisation of a cysteine peptidase from the invasive stage of the neuropathogenic schistosome Trichobilharzia regenti , 2009, International journal for parasitology.

[58]  Narmada Thanki,et al.  CDD: specific functional annotation with the Conserved Domain Database , 2008, Nucleic Acids Res..

[59]  Jan Dvorák,et al.  Chapter 4. Peptidases of trematodes. , 2009, Advances in parasitology.

[60]  Matthew P. Jacobson,et al.  Investigation of the Proteolytic Functions of an Expanded Cercarial Elastase Gene Family in Schistosoma mansoni , 2012, PLoS neglected tropical diseases.

[61]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .

[62]  John P. Overington,et al.  The genome of the blood fluke Schistosoma mansoni , 2009, Nature.

[63]  Alasdair C. Ivens,et al.  Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host , 2011, PLoS neglected tropical diseases.

[64]  Edward J. Pearce,et al.  Fatty Acid Oxidation Is Essential for Egg Production by the Parasitic Flatworm Schistosoma mansoni , 2012, PLoS pathogens.

[65]  Shengyue Wang,et al.  The genome of the hydatid tapeworm Echinococcus granulosus , 2013, Nature Genetics.

[66]  P. Ashton,et al.  Identification of Novel Proteases and Immunomodulators in the Secretions of Schistosome Cercariae That Facilitate Host Entry *S , 2006, Molecular & Cellular Proteomics.

[67]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[68]  Xing Wang Deng,et al.  The COP9 signalosome. , 2003, Annual review of cell and developmental biology.

[69]  M. Sajid,et al.  Schistosomiasis Mansoni: Novel Chemotherapy Using a Cysteine Protease Inhibitor , 2007, PLoS medicine.