Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome
© Bos et al; licensee BioMed Central Ltd. 2009
Received: 15 April 2009
Accepted: 21 October 2009
Published: 21 October 2009
New chemotherapeutic agents against Schistosoma mansoni, an etiological agent of human schistosomiasis, are a priority due to the emerging drug resistance and the inability of current drug treatments to prevent reinfection. Proteases have been under scrutiny as targets of immunological or chemotherapeutic anti-Schistosoma agents because of their vital role in many stages of the parasitic life cycle. Function has been established for only a handful of identified S. mansoni proteases, and the vast majority of these are the digestive proteases; very few of the conserved classes of regulatory proteases have been identified from Schistosoma species, despite their vital role in numerous cellular processes. To that end, we identified protease protein coding genes from the S. mansoni genome project and EST library.
We identified 255 protease sequences from five catalytic classes using predicted proteins of the S. mansoni genome. The vast majority of these show significant similarity to proteins in KEGG and the Conserved Domain Database. Proteases include calpains, caspases, cytosolic and mitochondrial signal peptidases, proteases that interact with ubiquitin and ubiquitin-like molecules, and proteases that perform regulated intramembrane proteolysis. Comparative analysis of classes of important regulatory proteases find conserved active site domains, and where appropriate, signal peptides and transmembrane helices. Phylogenetic analysis provides support for inferring functional divergence among regulatory aspartic, cysteine, and serine proteases.
Numerous proteases are identified for the first time in S. mansoni. We characterized important regulatory proteases and focus analysis on these proteases to complement the growing knowledge base of digestive proteases. This work provides a foundation for expanding knowledge of proteases in Schistosoma species and examining their diverse function and potential as targets for new chemotherapies.
Schistosomiasis is a common parasitic disease, affecting millions of people, mostly in tropical, developing countries . A causative agent of the disease is a trematode worm, Schistosoma mansoni. Treatment of schistosomiasis is commonly accomplished with praziquantel, for which the mechanism of action is not precisely defined but is thought to affect calcium ion channels  and/or purine nucleotide uptake . Despite the effectiveness of treatment, reinfection is common, and even more troubling, strains of S. mansoni resistant to praziquantel have been found . Thus, additional chemotherapeutic agents and an effective vaccine against this parasite have long been desired .
Ideally, vaccination of at-risk populations against the debilitating effects of schistosomiasis is desired, but no such treatment option is currently available. Surface receptors and other proteins are currently being tested for their potential to act as vaccines, but numerous challenges in the search for an effective vaccine have yet to be overcome . Some candidate vaccines are effective agents but cannot be mass produced. Most other candidate proteins have little potential as a vaccine, providing only 40-50% protection . While the search for an effective vaccine continues, it is critical to continue to identify molecular targets and their potential for chemotherapeutic disruption.
Proteases have been under scrutiny as targets of immunological or chemotherapeutic anti-Schistosoma agents because of their vital role in many stages of the parasitic life cycle [7, 8]. In addition, proteases are known to act as important regulatory elements in a variety of species [9, 10]. They also play a vital role as effectors of virulence in pathogens in general, often serving to alter host signal transduction and modify the immune response [11–14]. By targeting proteases specific to parasitic life style or those with significant dissimilarity to homologous proteases in the host species, investigators hope to find anti-schistosomal chemotherapies with minimal side effects to the host. However, few proteolytic enzymes have been purified in Schistosoma, and even fewer have well characterized functions and interactions.
Proteases of all five catalytic classes have been identified from Schistosoma species through proteomic or genetic analysis. Function has been established for only a handful of identified S. mansoni proteases, and the vast majority of these are the digestive proteases involved in metabolic food processing or host tissue penetration [15–18]. Additional proteases that are involved in reproduction, evasion of host immune system, and development have also been characterized [7, 19]. Very few proteases have been evaluated for the potential to serve as chemotherapeutic targets against schistosomiasis (e.g. ). Fortunately, it is almost certain that additional proteases exist in the S. mansoni genome, as the conserved classes of many regulatory proteases have not been identified from Schistosoma species. Since current therapies for a wide variety of disorders and diseases target regulatory molecules, such proteases may serve as new and effective targets for anti-helminthic treatments. The challenge of developing new therapies involves several steps, the first of which is to identify and characterize potential targets of drug or vaccine treatments. This is currently a task that is increasingly accomplished and streamlined with genomic and bioinformatic tools [9, 21].
The sequencing and annotation of the S. mansoni genome , combined with large EST libraries, provide a wealth of data from which to identify new vaccine or therapy targets [23–25]. These data, combined with bioinformatics tools and specialized databases, can fast-track the identification of potential anti-trematode agents by complementing and supplementing traditional genetic and proteomic identification techniques. Therefore, as an initial step in characterizing some of these potential targets, we survey the S. mansoni genome and EST library for protease genes. In doing so, we identify for the first time, numerous potentially important proteases in trematodes, many of which will have essential functions and may serve as targets of effective chemotherapeutic or immunological treatments.
Results and Discussion
Summary of characteristics from putative protease sequences from the Schistosoma mansoni genome.
Num. protease sequences
Num. protease families
Proteases with predicted transmembrane helices
Proteases with signal sequence
The recently published genome sequence of S. mansoni estimates the presence of 335 protease sequences in 60 families . For the protease families represented in both publications, estimated numbers are identical in 19 families, and 27 families are estimated by Berriman et al.  to have more members. In cases where estimates differ, most are very similar, the exception being families A01, C01, and S09, which we estimate to have a little more than half the previously published numbers. Such differences are easily attributed to differences in data mining methodologies. For instance, Berriman et al. used a Markov method to identify divergent homologues and culled sequences less than 80 residues or those that overlapped less than 50% of the most similar homologue. In comparison, our methods utilized no specialized methods to identify divergent homologues and culled sequences less than 100 residues or that overlapped less than 80% of the most similar homologue.
Below, we review the findings and highlight several important regulatory proteases which are identified for the first time in this species. We focus on regulatory proteases because numerous digestive proteases are already known and being studied in S. mansoni, but relatively little is known about the regulatory proteases despite their potential as targets for novel inhibitive chemotherapies.
Eleven loci encoding aspartic proteases from just three families were identified. Four of the aspartic proteases, all in the A1 family, were found to contain a signal peptide. Transmembrane (TM) predictions differed between methods: TMHMM found three proteases with a TM domain, all in family A22; TUPS detected a total of 5 TM domains among the A1 and A22 families (Table 1; see Additional file information 1). Two loci were significantly similar to family A2 proteases, but were subsequently found to lack similarity to any conserved domain, protease or not, in the CD database. We found five loci encoding proteins with high similarity to Pepsin/Cathepsin type aspartic proteases, which are broadly distributed among taxa and are most active at an acidic pH. Many of these sequences have already been identified in S. mansoni, and are known to be involved in digestion of host proteins . Other functions of this class of proteases are also known, and it is possible that specific sub-functions may be portioned among loci. However, only two of these loci show similarity to sequences in the S. mansoni EST library, so this possibility should be investigated further.
We also identify three A22 protease family members from S. mansoni for the first time. This class of proteases serves as important regulatory elements through their exceptional ability to lyse peptide bonds within a cell membrane . The capacity to lyse peptide bonds that lie embedded within a plasma membrane (also termed regulated intramembrane proteolysis, or RIP) is shared only among A22, M50 and S54 family proteases . These proteases associate with latent, membrane bound cell signaling molecules; upon intramembrane proteolysis, bioactive domains of the signaling molecules are freed to initiate a signaling cascade or act as an enzyme .
We detected 68 loci with significant similarity to known cysteine proteases; of these, 19% had an identifiable signal sequence and thus are likely to enter the secretory pathway. There was a large discrepancy between the two TM domain prediction algorithms: TMHMM found a TM domain in just one cysteine protease, whereas TUPs detected such a domain in 60% of the members of this catalytic class (Table 1). We detected 15 members of the C1 family of proteases, which contain the well-known cysteine-type cathepsin activity involved in digestion of host proteins . Eight of these loci had a conserved cathepsin B domain and other cathepsin family members were detected as well. Cathepsin proteases have already shown promise as targets of new anti-schistosomal therapies and further investigation is warranted . In addition to the digestive enzymes characterized by the cathepsins, we also detected numerous regulatory cysteine proteases.
Regulatory cysteine proteases include the calcium-dependent proteases typified by the calpain and caspase proteases. Calpain proteases belong to the C2 family, of which we found eight members encoded in the S. mansoni genome. Calpains are regulatory proteases with a broad array of functions and are involved in cell mobility, cell cycle progression, and the regulation of clotting factors. Calpains are one class of proteases already under investigation as vaccine candidates in S. japonicum, with results indicating a reduction in worm burden and egg production in immunized mice .
Identity matrix of selected caspase proteases
Another group of important regulatory elements include the cysteine proteases that interact with ubiquitin, SUMO and NEDD molecules (hereafter collectively referred to as ub-like). Ub-like molecules are known to function in the targeting of proteins for destruction by the 26S proteasome, but they also play a prominent regulatory role in the cell through post-translational modification, and protein turn-over and half life [40, 41]. We have putatively identified more than 30 members from the C12, C19, and C48 proteases families, which interact with ub-like protein molecules. These proteases are responsible for the activation (through cleavage of C-terminal di-glycine motifs) and recycling (by removing ub-like molecules from targeted proteins) of ubiquitin and SUMO molecules, controlling the regulatory roles these molecules play . For instance, ubiquitin is known in part to regulate apoptosis by antagonizing the reaction of caspases with the apoptosis complex; cleavage by ubiquitin proteases is central to this process .
It is interesting to note that some of the molecules that effect pathogenesis in bacteria use cysteine proteases that operate on host ub-like molecules to interfere with the regulation of proteins during infection . In fact, numerous effector proteins causing virulence in plant and animal pathogens such as Yersia and Pseudomonas are cysteine proteases, which target SUMO and other regulatory and signaling molecules such as NF-κB .
Metalloproteases make up a large fraction of proteolytic enzymes in the S. mansoni genome; one hundred loci were detected, and 12% of these contained signal sequence. Nineteen percent of metalloproteases have one or more trans-membrane alpha helices, indicating that a substantial portion of these proteases may be membrane bound (Table 1). The bioinformatic approach found a locus that may correspond to the previously identified LAP protease of family M17 . Additionally, we found a putative locus for a previously isolated protein thought to be the SmDPPIII, in family M28 . Many other metalloproteases, previously unidentified, were also detected.
There are hundreds of proteins that operate in the mitochondria, and the vast majority of them are encoded in the nucleus. The mitochondrial processing protease (MPP) and the mitochondrial intermediate protease (MIP) often function in concert to cleave signal peptides from immature mitochondrial proteins that are synthesized in the cytoplasm . Failure to do so obstructs further protein sorting, assembly, and function. We detected both the α- and β- (which should be catalytically active) subunits of the S. mansoni MPP. The β-MPP of S. mansoni has the conserved HxxEHx(76)E motif, indicating that it is probably catalytically active (Additional file 3). The S. mansoni α-MPP and the β-MPP share 20% identity, which is within the normal range of this comparison for several taxa. Interestingly, S. mansoni β-MPP shares 50% sequence identity with its human homolog, which is a higher similarity than the S. mansoni - C. elegans β-MPP homologs (40%).
A predicted protein for MIP was also detected, and contains a HExxH zinc binding domain, critical to catalysis. The putative S. mansoni MIP sequence contains 18 cysteine residues, consistent with cysteine enrichment in the MIP proteins of other species (human and rat MIPs have 18 and 16 cysteine residues respectively) . However, the C terminus of the protein truncates part of the larger catalytic domain conserved in this family of proteases, indicating that this sequence may either be artificially abbreviated by the gene prediction algorithms, or represent a pseudogene.
ATP-dependent mitochondrial proteases are also known, but their function is less well defined. Generally however, these play an essential role in quality control, turnover, and assembly of the respiratory chain complex proteins . Nine ATP-dependent proteases of the M41 family are detected in S. mansoni, and all contain an ATP binding motif, but only one sequence (Smp_165550) contains the active site HExxH motif. Treatment of S. mansoni with metalloprotease inhibitors results in unexplained paralysis of adult worms . This could be related to mitochondrial ATP-dependent protease inhibition, as defects or loss of this protease results in spastic paraplegia in humans and mice .
M50 family proteases are one of the three families of proteases that can perform RIP, and include mammalian S2P proteases, and bacterial SpoIVFB. One protease of the M50 family with an active site motif (HExxH) was detected in our analysis (Smp_054310). This protease is predicted to have multiple transmembrane helices, and the putative active site is found within the third transmembrane helix (approximately residues 175-195; see Additional file 3), consistent with predicted function . As with other proteases that perform RIP, bioactivation of the substrate is a multi-step process, involving multiple proteases. In mammals, S2P cannot perform RIP unless the substrate protein is first cleaved by S1P, a S08 family protease. A homolog of mammalian S1P is also found in S. mansoni, providing evidence of an active and at least partially conserved functional mechanism .
Sixty serine proteases were detected in our screening of the S. mansoni predicted proteins, and these are divided among 15 families. Sixteen loci were found to have a predicted signal sequence--many of these are in the S1 family, which is consistent with the majority of known S1 family proteases entering the secretory pathway and having a signal sequence. Twelve of the serine proteases have at least one transmembrane alpha helix, as predicted by TMHMM, whereas TUPs identified 35 proteases with a TM alpha helix (Table 1). We identified a locus for the well known cercarial elastase , and note that several loci also identified as having the highest similarity to cercarial elastase were detected, but were excluded from the analysis due to the likelihood of being pseudogenes. Numerous regulatory serine proteases are identified for the first time in S. mansoni with this report.
We also found members of the S08 family that have a catalytic mechanism that is distinct from the typical chymotrypsin activity of S01 family proteases. This family is mostly comprised of endoproteases with broad function, many of which enter the secretory pathway . S. mansoni also has S26 family members, which contain proteases that are responsible for processing numerous precursor proteins to active, mature forms . This occurs when signal peptides of newly synthesized proteins are cleaved upon arrival at a functional site. This cleavage event also acts as a post-translational regulatory event, controlling the activation of these proteins until the signal peptide is removed. Other AAA mitochondrial proteases of the S16 family, which bind DNA and RNA and may participate directly in the metabolism of mtDNA, are also found. Downregulation of this protease causes a general activation of caspases and leads to apoptosis .
We also found members of the S54 family of proteases in the S. mansoni genome. This family of proteases functions to perform RIP, resulting in the liberation of bioactive signaling peptides from anchoring TM domains [13, 59]. Consistent with the expected function, these S54 proteases have several TM helices predicted by both TMHMM and TUPs, indicating a likely conserved structure among taxa (Appendix 1).
Threonine proteases are most closely associated with the elements of the 20S proteasome, and the majority of threonine proteases discovered in our analysis appear to be subunits of that proteasome. At least 5 alpha subunits and 4 beta subunits of the proteasome were detected, all of which show evidence of being expressed. S. mansoni proteasome elements have already been identified and characterized through proteomic analysis, which detected all seven alpha and beta subunits and displayed morphological diversity due mainly to post-translational modifications . Thus, the bioinformatic data mining done here failed to identify all threonine protease genes present in the genome, or the genome annotation and gene detection methods used have failed to detect some genes known to be present. This difference highlights the need for collaborative work and the complementary nature of bioinformatic, and proteomic discovery of genetic elements.
In addition to the proteasome subunits, a taspase-like protease was identified in the S. mansoni genome. This protease cleaves the general transcription factor TFIIA, regulating transcription of numerous gene products.
We used in silico methods to explore the catalog of predicted proteins of S. mansoni for sequences homologous to known proteases. The search resulted in the detection of 255 putative proteases, over 90% of which are recognized for the first time in this species. Along with the proteases already described as having a function primarily in digestion and host invasion, we identify numerous previously unidentified regulatory proteases involved in a variety of biological processes. We focused on regulatory proteases because they generally serve essential functions in the maintenance of homeostasis and the developmental progression of the life cycle of a species. The vital nature of protease-mediated regulatory function underscores the potential of these proteases as targets of inhibitory chemotherapies and we hope that the identification of proteases stimulates further research into this area, such as expanding the application of gene silencing to identify the function of various proteases in Schistosoma species [62, 63].
We used the complete set of protease core sequences from the MEROPS (release 7.8) database  to identify putative homologues of known proteases in the S. mansoni genome. Core protease sequences comprise a non-redundant library of the catalytic unit of a protease and exclude all other functional units, such as ATP-binding, or calcium-binding domains. These sequences were used to avoid false positive identification of proteins as proteases due to high homology in non-catalytic parts of the sequence. Core sequences were compared to predicted proteins from the annotated S. mansoni genome. Release 4.0 of the S. mansoni genome includes a first-pass annotation and gene prediction, of which we downloaded the complete database of predicted proteins. In addition, the complete set of ESTs (release 6.0 of the S. mansoni gene index) isolated from 6 life stages of S. mansoni was also acquired.
Using the MEROPS proteases as the database, we used the predicted proteins as the query sequences in a local BLASTP  comparison. Default parameters were used during the search, where all predicted proteins were queried against all members of the protease database. In the comparison, only sequences with similarity scores <1e-04 were retained as S. mansoni protease homologs. From the initial result, query sequences identified as similar to homologous non-protease sequences (protease-like sequences but with mutations in active sites) were culled from the results, as were alternative splice forms of a gene. Additionally, predicted proteins that were shorter than 100 residues or less than 80% of the protease core sequence were not retained. Remaining sequences were subject to full analysis.
Results from the BLASTP query were subject to a number of analyses to characterize the sequences. We first independently sought the predicted function of S. mansoni sequences by searching for conserved motif and domains in the protein sequences. This was done using searches in the Conserved Domain Database (CDD) v. 2.13 of NCBI [66, 67]. CDD searches employ a reverse position-specific BLAST to align query sequence to protein domains from SMART v. 5.0 , Pfam v. 22.0 , and COG . The KEGG automated annotation server (KAAS) was used to assign pathway-based functional orthology to sequences in our dataset . We were also interested in identifying alpha-helix domains that likely span a cellular membrane. The prediction of these transmembrane helices is imprecise, so we report the results of two methods: TMHMM  and TUP .
The expected cellular location (e.g. cytoplasmic, membrane, or mitochondrial) and potential to enter the secretory pathway of a cell is also informative in classifying newly identified proteins. Therefore, we identified signal sequences in the proteins with signalP, using both the neural network and HMM methods [74, 75]. The D score is the average of the maximal Y-score (the most likely location of the cleavage site of the signal sequence) and the mean S-score, and is the best way to discriminate true signal sequences in proteins . Proteins with a D score greater than 55 and HMM greater than 90% were scored as having an N-terminal signal sequence and the Y-score was recorded for these proteins. We used the eukaryote setting with each sequence truncated after 70 residues to avoid false positive detection of signal sequence outside of the N-terminus.
Functionally distinct proteases may show differential phylogenetic clustering. Therefore, we performed phylogenetic comparisons, including mainly species with functionally defined proteases with S. mansoni sequences (accession numbers of sequences used are given in the Additional files). While phylogenetic analysis does detect evidence of divergence, the functional implications of the divergence must be tested experimentally, as such phylogenetic analyses represent an initial assessment of potential functional divergence among multiple S. mansoni proteases within a family. For phylogenetic analysis, homologous protein sequences from selected species were obtained from NCBI GENBANK. Alignments were made using MUSCLE default parameters . Resulting alignments were subject to phylogenetic analysis using MRBAYES . Flexible priors were used by employing a mixed model analysis. Mixed model analysis avoids reliance on a single model of amino acid substitutions (and thus a single prior) by allowing the MCMC sampler to regularly propose and explore the fit of new models during analysis (see MRBAYES documentation for model specifications). Each model contributes to the results in proportion to their posterior probability. We performed two simultaneous but independent runs on each data set, with each run consisting of three heated chains and one cold chain. Runs were continued until the average standard deviation of the split frequencies between the two runs was less than 0.02, with a minimum of 100,000 MCMC generations. Trees were sampled every 50th generation, resulting in at least 2,000 saved trees. The first 25% of trees were discarded as burn-in prior to summarizing sampled trees. Summarizing samples produced a consensus tree with branch bifurcation support (clade credibility) indicated. Clade credibility was calculated for each bifurcation as the proportion of sampled trees with that bifurcation.
We thank the Minchella lab members for support and comments on earlier versions of this manuscript. We thank insightful and constructive editorial and reviewer comments, which have improved this manuscript. This work is funded by National Institute of Health grant #R01-AI-42768 to DJM.
- Chitsulo L, Engels D, Montresor A, Savioli L: The global status of schistosomiasis and its control. Acta Tropica. 2000, 77: 41-51. 10.1016/S0001-706X(00)00122-4.View ArticlePubMedGoogle Scholar
- Kohn AB, Roberts-Misterly JM, Anderson PAV, Kahn N, Greenberg RM: Specific sites in the Beta interaction domain of a schisomsome Ca2+ channel β subunit are key to its role in sensitivity to the anti-schistosomal drug praziquantel. Parasitology. 2003, 127: 349-356. 10.1017/S003118200300386X.View ArticlePubMedGoogle Scholar
- Angelucci F, Basso A, Bellelli A, Brunori M, Pica Mattoccia L, Valle C: The anti-schistosomal drug praziquantel is an adenosine antagonist. Parasitology. 2007, 134: 1215-1221. 10.1017/S0031182007002600.View ArticlePubMedGoogle Scholar
- Ismail M, Botros S, Metwally A, William S, Farghally A, Tao L, Day T, Bennett J: Resistance to praziquantel: direct evidence from Schistosoma mansoni isolated from Egyptian villagers. American Journal of Tropical Medicine and Hygiene. 1999, 60 (6): 932-935.PubMedGoogle Scholar
- Engels D, Chitsulo L, Montresor A, Savioli L: The global epidemiological situation of schistosomiasis and new approaches to control and research. Acta Tropica. 2002, 82 (2): 139-146. 10.1016/S0001-706X(02)00045-1.View ArticlePubMedGoogle Scholar
- McManus DP: Prospects for development of a transmission blocking vaccine against Schistosoma japonicum. Parasite Immunology. 2005, 27: 297-308. 10.1111/j.1365-3024.2005.00784.x.View ArticlePubMedGoogle Scholar
- Klemba M, Goldberg DE: Biological roles of proteases in parasitic protozoa. Ann Rev Biochem. 2002, 71 (1): 275-305. 10.1146/annurev.biochem.71.090501.145453.View ArticlePubMedGoogle Scholar
- Dalton JP, Brindley PJ: Proteases of Trematodes. Trematode Biology. Edited by: Fried B, Graczyk TK. 1997, Boca Raton: CRC Press, 265-307.Google Scholar
- Turk B: Targeting proteases: successes, failures and future prospects. Nature Reviews Drug Discovery. 2006, 5 (9): 785-799. 10.1038/nrd2092.View ArticlePubMedGoogle Scholar
- Ehrmann M, Clausen T: Proteolysis as a regulatory mechanism. Ann Rev Genet. 2004, 38: 709-724. 10.1146/annurev.genet.38.072902.093416.View ArticlePubMedGoogle Scholar
- Niu Q, Huang X, Zhang L, Li Y, Li J, Yang J, Zhang K: A neutral protease from Bacillus nematocida, another potential virulence factor in the infection against nematodes. Archives of Microbiology. 2006, 185 (6): 439-448. 10.1007/s00203-006-0112-x.View ArticlePubMedGoogle Scholar
- McKerrow JH, Caffrey C, Kelly B, Loke Pn, Sajid M: Proteases in parasitic diseases. Annu Rev Pathol. 2006, 1: 497-536. 10.1146/annurev.pathol.1.110304.100151.View ArticlePubMedGoogle Scholar
- Urban S: Rhomboid proteins: conserved membrane proteases with divergent biological functions. Genes Dev. 2006, 20 (22): 3054-3068. 10.1101/gad.1488606.View ArticlePubMedGoogle Scholar
- Hotson A, Mudgett MB: Cysteine proteases in phytophathogenic bacteria: identification of plant targets and activation of innate immunity. Current Opinion in Plant Biology. 2004, 7: 384-390. 10.1016/j.pbi.2004.05.003.View ArticlePubMedGoogle Scholar
- Williamson AL, Brindley PJ, Knox DP, Hotez PJ, Loukas A: Digestive proteases of blood-feeding nematodes. Trends in Parasitology. 2003, 19 (9): 417-423. 10.1016/S1471-4922(03)00189-2.View ArticlePubMedGoogle Scholar
- Curwen RS, Ashton PD, Sundaralingam S, Wilson RA: Identification of Novel Proteases and Immunomodulators in the Secretions of Schistosome Cercariae That Facilitate Host Entry. Molecular and Cellular Proteomics. 2006, 5 (5): 835-844. 10.1074/mcp.M500313-MCP200.View ArticlePubMedGoogle Scholar
- McKerrow J, Salter J: Invasion of skin by Schistosoma cercariae. Trends in Parasitology. 2002, 18 (5): 193-195. 10.1016/S1471-4922(02)02309-7.View ArticlePubMedGoogle Scholar
- Delcroix M, Sajid M, Caffrey CR, Lim K-C, Dvorak J, Hsieh I, Bahgat M, Dissous C, McKerrow JH: A multienzyme network functions in intestinal protein digestion by a Platyhelminth parasite. J Biol Chem. 2006, 281 (51): 39316-39329. 10.1074/jbc.M607128200.View ArticlePubMedGoogle Scholar
- Tort J, Brindley PJ, Knox D, Wolfe KH, Dalton JP: Proteinases and associated genes of parasitic helminths. Advances in Parasitology. 1999, 43: 161-266. full_text.View ArticlePubMedGoogle Scholar
- Zhang R, Yoshida A, Kumagai T, Kawaguchi H, Maruyama H, Suzuki T, Itoh M, El-Malky M, Ohta N: Vaccination with calpain induces a Th1-biased protective immune response against Schistosoma japonicum. Infection and Immunity. 2001, 69 (1): 386-391. 10.1128/IAI.69.1.386-391.2001.PubMed CentralView ArticlePubMedGoogle Scholar
- Southan C, Ulvsback M, Barnes MR: A bioinformatics perspective on genetics in drug discovery and development. Bioinformatics for Geneticists. Edited by: Barnes MR. 2007, West Sussex: John Wiley & Sons, SecondGoogle Scholar
- Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, et al: The genome of the blood fluke Schistosoma mansoni. Nature. 2009, 460 (7253): 352-358. 10.1038/nature08160.PubMed CentralView ArticlePubMedGoogle Scholar
- Hu W, Brindley PJ, McManus DP, Feng Z, Han ZG: Schistosome transcriptomes: new insights into the parasite and schistosomiasis. Trends in Molecular Medicine. 2004, 10 (5): 217-225. 10.1016/j.molmed.2004.03.002.View ArticlePubMedGoogle Scholar
- Verjovski-Almeida S, DeMarco R, Martins EAL, Guimaraes PEM, Ojopi EPB, Paquola ACM, Piazza JP, Nishiyama MY, Kitajima JP, Adamson RE, et al: Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genet. 2003, 35 (2): 148-157. 10.1038/ng1237.View ArticlePubMedGoogle Scholar
- Liu F, Lu J, Hu W, Wang SY, Cui SJ, Chi M, Yan Q, Wang XR, Song HD, Xu XN, et al: New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathogens. 2006, 2 (4): e29-10.1371/journal.ppat.0020029.PubMed CentralView ArticlePubMedGoogle Scholar
- Southan C: A genomic perspective on human proteases. FEBS Letters Lisbon Special Issue. 2001, 498 (2-3): 214-218.View ArticleGoogle Scholar
- Puente XS, Sanchez LM, Overall CM, Lopez-Otin C: Human and mouse proteases: a comparative genomic approach. Nature Rev Genet. 2003, 4 (7): 544-558. 10.1038/nrg1111.View ArticlePubMedGoogle Scholar
- Caffrey CR, McKerrow JH, Salter JP, Sajid M: Blood 'n' guts: an update on schistosome digestive peptidases. Trends in Parasitology. 2004, 20 (5): 241-248. 10.1016/j.pt.2004.03.004.View ArticlePubMedGoogle Scholar
- Weihofen A, Binns K, Lemberg MK, Ashman K, Martoglio B: Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science. 2002, 296 (5576): 2215-2218. 10.1126/science.1070925.View ArticlePubMedGoogle Scholar
- Wolfe MS, Kopan R: Intramembrane proteolysis: theme and variations. Science. 2004, 305 (5687): 1119-1123. 10.1126/science.1096187.View ArticlePubMedGoogle Scholar
- Brown MS, Ye J, Rawson RB, Goldstein JL: Regulated intramembrane proteolysis: a control mechanism conserved from bacteria to humans. Cell. 2000, 100: 391-398. 10.1016/S0092-8674(00)80675-3.View ArticlePubMedGoogle Scholar
- Westlund B, Parry D, Clover R, Basson M, Johnson CD: Reverse genetic analysis of Caenorhabditis elegans presenilins reveals redundant but unequal roles for sel-12 and hop-1 in Notch-pathway signaling. Proc Natl Acad Sci U S A. 1999, 96 (5): 2497-2502. 10.1073/pnas.96.5.2497.PubMed CentralView ArticlePubMedGoogle Scholar
- Grigorenko AP, Moliaka YK, Soto MC, Mello CC, Rogaev EI: The Caenorhabditis elegans IMPAS gene, imp-2, is essential for development and is functionally distinct from related presenilins. Proc Natl Acad Sci USA. 2004, 101 (41): 14955-14960. 10.1073/pnas.0406462101.PubMed CentralView ArticlePubMedGoogle Scholar
- Braud VM, Allan DSJ, O'Callaghan CA, Soderstrom K, D'Andrea A, Ogg GS, Lazetic S, Young NT, Bell JI, Phillips JH, et al: HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C. Nature. 1998, 391 (6669): 795-799. 10.1038/35869.View ArticlePubMedGoogle Scholar
- Abdulla MH, Lim KC, Sajid M, McKerrow JH, Caffrey CR: Schistosomiasis Mansoni: novel chemotherapy using a cysteine protease inhibitor. PLos Medicine. 2007, 4 (1): e14-10.1371/journal.pmed.0040014.PubMed CentralView ArticlePubMedGoogle Scholar
- Yuan J, Shaham S, Ledoux S, Ellis HM, Horvitz HR: The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme. Cell. 1993, 75: 641-652. 10.1016/0092-8674(93)90485-9.View ArticlePubMedGoogle Scholar
- Abraham MC, Shaham S: Death without caspases, caspases without death. Trends in Cell Biology. 2004, 14 (4): 184-193. 10.1016/j.tcb.2004.03.002.View ArticlePubMedGoogle Scholar
- Lamkanfi M, Declercq W, Kalai M, Saelens X, Vandenabeele P: Alice in caspaseland. A phylogenetic analysis of caspases from worm to man. Cell Death and Differentiation. 2002, 9: 358-361. 10.1038/sj.cdd.4400989.View ArticlePubMedGoogle Scholar
- Michalke M, Stepczynska A, Burek M, Nguyen Bui T, Loser K, Krzemieniecki K, Los M: Caspases as Targets for Drug Development. Caspases: Their Role in Cell Death and Cell Survival. Edited by: Los M, Walczak H. 2003, New York: Kluwer Academic/Plenum Publishers, 221-236.Google Scholar
- Bowerman B, Kurz T: Degrade to create: developmental requirements for ubiquitin-mediated proteolysis during early C. elegans embryogenesis. Development. 2006, 133 (5): 773-784. 10.1242/dev.02276.View ArticlePubMedGoogle Scholar
- Geiss-Friedlander R, Melchior F: Concepts in sumoylation: a decade on. Nature Reviews Molecular Cell Biology. 2007, 8 (12): 947-956. 10.1038/nrm2293.View ArticlePubMedGoogle Scholar
- Mukhopadhyay D, Dasso M: Modification in reverse: the SUMO proteases. Trends Biochem Sci. 2007, 32 (6): 286-295. 10.1016/j.tibs.2007.05.002.View ArticlePubMedGoogle Scholar
- Ditzel M, Meier P: IAP degradation: decisive blow or altruistic sacrifice?. Trends in Cell Biology. 2002, 12 (10): 449-452. 10.1016/S0962-8924(02)02366-8.View ArticlePubMedGoogle Scholar
- Hotson A, Chosed R, Shu H, Orth K, Mudgett MB: Xanthomonas type III effector XopD targets SUMO-conjugated proteins in planta. Molecular Microbiology. 2003, 50 (2): 377-389. 10.1046/j.1365-2958.2003.03730.x.View ArticlePubMedGoogle Scholar
- Xu YZ, Dresden MH: Leucine amino-peptidase and hatching of Schistosoma mansoni eggs. Journal of Parasitology. 1986, 72: 507-511. 10.2307/3281498.View ArticlePubMedGoogle Scholar
- Hola-Jamriska L, Dalton JP, Aaskov J, Brindley PJ: Dipeptidyl peptidase I and II activities of adult schistosomes. Parasitology. 1999, 118: 275-282. 10.1017/S0031182098003746.View ArticlePubMedGoogle Scholar
- Gakh O, Cavadini P, Isaya G: Mitochondrial processing peptidases. Biochim Biophys Acta. 2002, 1592 (1): 63-77. 10.1016/S0167-4889(02)00265-3.View ArticlePubMedGoogle Scholar
- Arnold I, Langer T: Membrane protein degradation by AAA proteases in mitochondria. Biochim Biophys Acta. 2002, 1592 (1): 89-96. 10.1016/S0167-4889(02)00267-7.View ArticlePubMedGoogle Scholar
- Day TA, Chen GZ: The metalloprotease inhibitor 1,10-phenanthroline affects Schistosoma mansoni motor activity, egg laying and viability. Parasitology. 1998, 116: 319-325. 10.1017/S0031182097002370.View ArticlePubMedGoogle Scholar
- Nolden M, Ehses S, Koppen M, Bernacchia A, Rugarli EI, Langer T: The m-AAA protease defective in hereditary spastic paraplegia controls ribosome assembly in mitochondria. Cell. 2005, 123 (2): 277-289. 10.1016/j.cell.2005.08.003.View ArticlePubMedGoogle Scholar
- Kinch LN, Ginalski K, Grishin NV: Site-2 protease regulated intramembrane proteolysis: Sequence homologs suggest an ancient signaling cascade. Protein Science. 2006, 15 (1): 84-93. 10.1110/ps.051766506.PubMed CentralView ArticlePubMedGoogle Scholar
- Salter JP, Lim KC, Hansell E, Hsieh I, McKerrow JH: Schistosome invasion of human skin and degradation of dermal elastin are mediated by a single serine protease. J Biol Chem. 2000, 275 (49): 38667-38673. 10.1074/jbc.M006997200.View ArticlePubMedGoogle Scholar
- Krem MM, Di Cera E: Molecular markers of serine protease evolution. EMBO Journal. 2001, 20 (12): 3036-3045. 10.1093/emboj/20.12.3036.PubMed CentralView ArticlePubMedGoogle Scholar
- Krem MM, Rose T, Di Cera E: The C-terminal Sequence Encodes Function in Serine Proteases. J Biol Chem. 1999, 274 (40): 28063-28066. 10.1074/jbc.274.40.28063.View ArticlePubMedGoogle Scholar
- Rose T, Di Cera E: Substrate Recognition Drives the Evolution of Serine Proteases. J Biol Chem. 2002, 277 (22): 19243-19246. 10.1074/jbc.C200132200.View ArticlePubMedGoogle Scholar
- Siezen RJ, Leunissen JA: Subtilases: the superfamily of subtilisin-like serine proteases. Protein Science. 1997, 6 (3): 501-523.PubMed CentralView ArticlePubMedGoogle Scholar
- Dalbey RE, von Heijne G: Signal peptidases in prokaryotes and eukaryotes - a new protease family. Trends Biochem Sci. 1992, 17 (11): 474-478. 10.1016/0968-0004(92)90492-R.View ArticlePubMedGoogle Scholar
- Bota DA, Ngo JK, Davies KJA: Downregulation of the human Lon protease impairs mitochondrial structure and function and causes cell death. Free Radical Biology and Medicine. 2005, 38 (5): 665-677. 10.1016/j.freeradbiomed.2004.11.017.View ArticlePubMedGoogle Scholar
- Urban S, Wolfe MS: Reconstitution of intramembrane proteolysis in vitro reveals that pure rhomboid is sufficient for catalysis and specificity. Proc Natl Acad Sci U S A. 2005, 102 (6): 1883-1888. 10.1073/pnas.0408306102.PubMed CentralView ArticlePubMedGoogle Scholar
- Lemberg MK, Freeman M: Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases. Genome Res. 2007, 17 (11): 1634-1646. 10.1101/gr.6425307.PubMed CentralView ArticlePubMedGoogle Scholar
- Castro-Borges W, Cartwright J, Ashton PD, Braschi S, Sa RG, Rodrigues V, Wilson RA, Curwen RS: The 20S proteasome of Schistosoma mansoni: a proteomic analysis. Proteomics. 2007, 7: 1065-1075. 10.1002/pmic.200600166.View ArticlePubMedGoogle Scholar
- Krautz-Peterson G, Magdalena R, Ndegwa D, Shoemaker CB, Skelly PJ: Optimizing gene suppression in schistosomes using RNA interference. Molecular and Biochemical Parasitology. 2007, 153: 194-202. 10.1016/j.molbiopara.2007.03.006.View ArticlePubMedGoogle Scholar
- Morales ME, Rinaldi G, Gobert GN, Kines KJ, Tort JF, Brindley PJ: RNA interference of Schistosoma mansoni cathepsin D, the apical enzyme of the hemoglobin proteolysis cascade. Molecular and Biochemical Parasitology. 2008, 157: 160-168. 10.1016/j.molbiopara.2007.10.009.PubMed CentralView ArticlePubMedGoogle Scholar
- Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ: MEROPS: the peptidase database. Nucleic Acids Res. 2008, 36: D320-D325. 10.1093/nar/gkm954.PubMed CentralView ArticlePubMedGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.View ArticlePubMedGoogle Scholar
- Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z: CDD, et al: a Conserved Domain Database for protein classification. Nucleic Acids Res. 2005, 33 (suppl_1): D192-196.PubMed CentralPubMedGoogle Scholar
- Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH: CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002, 30 (1): 281-283. 10.1093/nar/30.1.281.PubMed CentralView ArticlePubMedGoogle Scholar
- Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P: SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 2006, 34 (suppl_1): D257-260. 10.1093/nar/gkj079.PubMed CentralView ArticlePubMedGoogle Scholar
- Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al: Pfam: clans, web tools and services. Nucleic Acids Res. 2006, 34 (suppl_1): D247-251. 10.1093/nar/gkj149.PubMed CentralView ArticlePubMedGoogle Scholar
- Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Mekhedov S, Nikolskaya A, et al: The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003, 4 (1): 41-10.1186/1471-2105-4-41.PubMed CentralView ArticlePubMedGoogle Scholar
- Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M: KAAS: an automated genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007, W182-W185. 10.1093/nar/gkm321. 35 Web ServerGoogle Scholar
- Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: applications to complete genomes. J Mol Biol. 2001, 305 (3): 567-580. 10.1006/jmbi.2000.4315.View ArticlePubMedGoogle Scholar
- Zhou H, Zhou Y: Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model based method. Protein Science. 2003, 12: 1547-1555. 10.1110/ps.0305103.PubMed CentralView ArticlePubMedGoogle Scholar
- Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004, 340: 783-795. 10.1016/j.jmb.2004.05.028.View ArticlePubMedGoogle Scholar
- Nielsen H, Brunak S, Engelbrecht J, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering. 1997, 10: 1-6. 10.1093/protein/10.1.1.View ArticlePubMedGoogle Scholar
- Emanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols. 2007, 2 (4): 953-971. 10.1038/nprot.2007.131.View ArticlePubMedGoogle Scholar
- Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5: 113-10.1186/1471-2105-5-113.PubMed CentralView ArticlePubMedGoogle Scholar
- Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19 (12): 1572-1574. 10.1093/bioinformatics/btg180.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.