BACKGROUND
schistosomiasis is a common parasitic disease, affecting millions of people, mostly in tropical, developing countries  <cit> .
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  <cit>  and/or purine nucleotide uptake  <cit> .
despite the effectiveness of treatment, reinfection is common, and even more troubling, strains of s. mansoni resistant to praziquantel have been found  <cit> .
thus, additional chemotherapeutic agents and an effective vaccine against this parasite have long been desired  <cit> .
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  <cit> .
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  <cit> .
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  <cit> .
in addition, proteases are known to act as important regulatory elements in a variety of species  <cit> .
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  <cit> .
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  <cit> .
additional proteases that are involved in reproduction, evasion of host immune system, and development have also been characterized  <cit> .
very few proteases have been evaluated for the potential to serve as chemotherapeutic targets against schistosomiasis .
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  <cit> .
the sequencing and annotation of the s. mansoni genome  <cit> , combined with large est libraries, provide a wealth of data from which to identify new vaccine or therapy targets  <cit> .
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
after culling the data of redundant sequences, inactive homologs and likely pseudogenes, we identified a total of  <dig> predicted proteases among  <dig> families .
the  <dig> proteases identified here comprise  <dig> % of the roughly  <dig>  predicted genes in the s. mansoni genome  <cit> .
in the merops database, there are currently  <dig> known or putative proteases identified in s. mansoni.
since over 90% of the genes presented here are new, this bioinformatic data mining represents a substantial expansion of putative proteases from this species.
as expected, proteases of five catalytic classes were identified: 4% are aspartic, 26% are cysteine, 39% are metalloproteases, 24% are serine, and 6% are threonine proteases.
these proportions are largely in harmony with those from other organisms  <cit> .
the recently published genome sequence of s. mansoni estimates the presence of  <dig> protease sequences in  <dig> families  <cit> .
for the protease families represented in both publications, estimated numbers are identical in  <dig> families, and  <dig> families are estimated by berriman et al.
<cit>  to have more members.
in cases where estimates differ, most are very similar, the exception being families a <dig>  c <dig>  and s <dig>  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  <dig> 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  <dig> residues or that overlapped less than 80% of the most similar homologue.
comparatively, caenorhabditis elegans, a round worm with a well characterized and annotated genome, has  <dig> known or putative proteases in the merops database.
the proportions of classes of proteases are roughly equivalent, but we note a slight expansion in the relative proportion of serine proteases in c. elegans compared to s. mansoni, and a comparative expansion of cysteine proteases in s. mansoni .
some differences will also naturally arise because of differences in organism complexity and life style .
however, differences between these two species may also partially be attributable to the coverage and sequence quality of the genomes, and the fact that s. mansoni genome characterizations are newer and still very much subject to verification and basic delineation.
most of the protein sequences that had high similarity to merops database sequences were verified as having a conserved protease-specific domain .
kaas was able to assign orthology and kegg functional pathways to  <dig> of the s. mansoni proteases .
forty-one proteases are assigned to be involved in metabolic processes, while twenty-four are involved in genetic information processing.
environmental information processes involve eleven proteases, while eleven additional proteases are engaged in cellular processes such as communication and cell cycling.
we note that despite the removal of sequences that show similarity to inactive proteases in merops, and assignment of sequences to functional pathways, none of the new proteases identified in the present work have been experimentally shown to be catalytically active.
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.
aspartic proteases
eleven loci encoding aspartic proteases from just three families were identified.
four of the aspartic proteases, all in the a <dig> family, were found to contain a signal peptide.
transmembrane  predictions differed between methods: tmhmm found three proteases with a tm domain, all in family a22; tups detected a total of  <dig> tm domains among the a <dig> and a <dig> families .
two loci were significantly similar to family a <dig> 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  <cit> .
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 a <dig> 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  <cit> .
the capacity to lyse peptide bonds that lie embedded within a plasma membrane  is shared only among a <dig>  m <dig> and s <dig> family proteases  <cit> .
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  <cit> .
the s. mansoni a <dig> protease smp_ <dig> contains both active site motifs, and in a phylogeny  is closely associated with presenilin-type proteases from c. elegans.
the conserved evolutionary function of presenilin proteases is the control of notch proteins, which act as regulators of gene expression and are involved in diverse cellular and tissue functions such as cell maturation, angiogenesis, and neuronal function and development  <cit> .
smp_ <dig> also contains both active site motifs, but forms part of a clade comprised of signal peptide proteases.
the signal peptide proteases  are not associated with notch signaling in c. elegans, but are involved in embryonic development and larval molting  <cit> .
impas protease knockout c. elegans have an embryonic lethal phenotype, possibly due to the function of the protease in lipid homeostasis and the production of cholesterol-derived hormones.
thus it is significant that smp_ <dig> clusters with other signal peptide proteases, which are nonredundant and distinct from presenilin protease activity.
the remaining a <dig> protease from s. mansoni, smp_ <dig>  does not contain the complete catalytic dyad .
smp_ <dig> is not allied closely in the phylogenetic tree with either presenilin or signal peptide proteases  but the genetic distance shows it shares higher sequence similarity to smp_ <dig> .
interestingly, a <dig> family proteases cleave the signal peptides of mhc class i molecules  in humans, which serve as a ligand for hla-e molecules.
this activity reports successful mhc biosynthesis to the immune system and regulates nk cell mediated attack  <cit> .
cysteine proteases
we detected  <dig> 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 .
we detected  <dig> members of the c <dig> family of proteases, which contain the well-known cysteine-type cathepsin activity involved in digestion of host proteins  <cit> .
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  <cit> .
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 c <dig> 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  <cit> .
caspase proteases are also calcium-dependent, and are most prominently known to control apoptosis in a wide variety of animals, including other bilaterian worms  <cit> .
however, the so called inflammatory caspases mediate non-death functions such as inflammation, immunity, and maturation of a variety of cell types  <cit> .
although there is broad overlap, apoptosis caspases are often categorized as initiator , and effector caspases .
the four s. mansoni caspases identified here all have the conserved catalytic motifs of his-gly and ala-cys, and are preceded by blocks of hydrophobic residues .
c. elegans also has  <dig> caspase loci, but only three have a conserved catalytic motif.
in a sequence identity matrix of s. mansoni, c. elegans and human caspases, all of the s. mansoni caspases shared more similarity to caspases from humans rather than to any other species, including other s. mansoni caspases .
in three out of the four cases, s. mansoni shared their highest similarity to human caspases, whereas all human caspases except one were most similar to another human caspase.
caspases fall into three phylogenetic clades, which largely correspond with tetrapeptide substrate specificity  <cit> .
caspases from a species typically fall into multiple clades, with the known exception being c. elegans, whose caspases also form a species-specific clade in our phylogenetic analysis.
s. mansoni caspases are dispersed among the three clades , as seen in most species, but unlike c. elegans.
two s. mansoni caspases  are in a clade with effector caspases from humans and mice, while smp_ <dig> is associated with classical initiators caspase  <dig> and caspase  <dig>  the fourth trematode caspase is in a monophyletic group with the initiator caspase  <dig>  and a larger clade of mostly inflammatory caspases, which have a regulatory role in the immune system and are associated only with species having a complex hematopoesis involved in the immune response.
the placement of s. mansoni caspases in the larger phylogeny raises interesting possibilities regarding the specificity and function of these proteases which warrants further investigation.
although caspases are important regulatory proteins and are targets of chemotherapeutic agents in several pathologies, including cancer  <cit> , no anti-schistosomal agents are currently being investigated that target these proteases.
another group of important regulatory elements include the cysteine proteases that interact with ubiquitin, sumo and nedd molecules .
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  <cit> .
we have putatively identified more than  <dig> members from the c <dig>  c <dig>  and c <dig> proteases families, which interact with ub-like protein molecules.
these proteases are responsible for the activation  and recycling  of ubiquitin and sumo molecules, controlling the regulatory roles these molecules play  <cit> .
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  <cit> .
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  <cit> .
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  <cit> .
metalloproteases
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 .
the bioinformatic approach found a locus that may correspond to the previously identified lap protease of family m <dig>  <cit> .
additionally, we found a putative locus for a previously isolated protein thought to be the smdppiii, in family m <dig>  <cit> .
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  and the mitochondrial intermediate protease  often function in concert to cleave signal peptides from immature mitochondrial proteins that are synthesized in the cytoplasm  <cit> .
failure to do so obstructs further protein sorting, assembly, and function.
we detected both the α- and β-  subunits of the s. mansoni mpp.
the β-mpp of s. mansoni has the conserved hxxehxe motif, indicating that it is probably catalytically active .
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 .
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  <dig> cysteine residues, consistent with cysteine enrichment in the mip proteins of other species   <cit> .
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  <cit> .
nine atp-dependent proteases of the m <dig> family are detected in s. mansoni, and all contain an atp binding motif, but only one sequence  contains the active site hexxh motif.
treatment of s. mansoni with metalloprotease inhibitors results in unexplained paralysis of adult worms  <cit> .
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  <cit> .
m <dig> 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 m <dig> family with an active site motif  was detected in our analysis .
this protease is predicted to have multiple transmembrane helices, and the putative active site is found within the third transmembrane helix , consistent with predicted function  <cit> .
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 s <dig> 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  <cit> .
serine proteases
sixty serine proteases were detected in our screening of the s. mansoni predicted proteins, and these are divided among  <dig> families.
sixteen loci were found to have a predicted signal sequence--many of these are in the s <dig> family, which is consistent with the majority of known s <dig> 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  <dig> proteases with a tm alpha helix .
we identified a locus for the well known cercarial elastase  <cit> , 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.
the s <dig> family is the largest group of proteases, with a wide variety of functions.
this functional divergence is frequently reflected in phylogenetic grouping and/or variation at 5- <dig> base-pair motifs surrounding functionally important residues, such as active sites  <cit> .
we identified eighteen s <dig> proteases in the s. mansoni genome, however six of these did not have a significant similarity to a conserved protease domain .
in addition, alignment of the sequences revealed that only seven of these predicted proteins have the conserved catalytic triad of his, asp, and ser .
a phylogeny of s <dig> proteases from human, drosophila, c. elegans, and s. mansoni resulted in a general lack of resolution in the deeper nodes, making it difficult to ascertain any level of functional clustering .
despite this, a strongly supported cluster of four s. mansoni proteases  is formed among sequences with 58-99% identity.
included in this cluster are cercarial elastase and other proteases of similar predicted length.
two of the remaining s. mansoni s <dig> proteases are in a large unresolved polytomy that includes s <dig> proteases from all species included in the analysis.
the final s. mansoni s <dig> protease is in a clade of "effector" proteases that function downstream in a signaling cascade and operate on cellular substrates .
although it is impossible to assign functions to s. mansoni s <dig> proteases through the above analysis, results indicate a possible functional divergence among s. mansoni s <dig> proteases.
some of these sequences may have a closely related  function that is not shared with other organisms included in the analysis.
we also found members of the s <dig> family that have a catalytic mechanism that is distinct from the typical chymotrypsin activity of s <dig> family proteases.
this family is mostly comprised of endoproteases with broad function, many of which enter the secretory pathway  <cit> .
s. mansoni also has s <dig> family members, which contain proteases that are responsible for processing numerous precursor proteins to active, mature forms  <cit> .
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 s <dig> 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  <cit> .
we also found members of the s <dig> 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  <cit> .
consistent with the expected function, these s <dig> proteases have several tm helices predicted by both tmhmm and tups, indicating a likely conserved structure among taxa .
s <dig> family proteases are termed rhomboid proteases and can be divided into several groups because of conserved structure, substrate similarity, and cellular localization.
these differences are reflected in their phylogenetic clustering into parl, secretase, and irhom-type proteases  <cit> .
we included putative s. mansoni rhomboid proteases in phylogenetic analysis to categorize these into subtypes and as an initial assessment of similarity and possible function .
the resulting phylogenetic tree strongly supported groups corresponding to parl, secretase, and irhom proteases, but the relationships within and among the three groups were not always clear.
the three s. mansoni putative rhomboid family members fell into three separate clades.
smp_ <dig> has the conserved histidine and gxsx motif in a hydrophobic region predicted to be in a transmembrane helix .
this is characteristic of proteolytically active rhomboids and smp_ <dig> was placed with the parl-like proteases, which localize to the mitochondria.
smp_ <dig> clusters with the secretase-a rhomboids, and consistent with this clustering is the conserved catalytic motif in a hydrophobic region.
smp_ <dig> is short and likely represents an incomplete sequence, but portions of it do show significant similarity to irhom-like rhomboids, including a conserved proline in the degenerate catalytic motif.
irhoms lack a catalytic activity, but their phylogenetic clustering suggests some conserved functional relationship.
these assessments of s. mansoni rhomboids to functional classes are simply based on similarity and await experimental confirmation.
threonine proteases
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  <dig> alpha subunits and  <dig> 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  <cit> .
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.
CONCLUSIONS
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  <dig> 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  <cit> .

 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. in addition, proteases are known to act as important regulatory elements in a variety of species. 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. 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. additional proteases that are involved in reproduction, evasion of host immune system, and development have also been characterized. very few proteases have been evaluated for the potential to serve as chemotherapeutic targets against schistosomiasis. 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. 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. 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.  after culling the data of redundant sequences, inactive homologs and likely pseudogenes, we identified a total of predicted proteases among families. the proteases identified here comprise % of the roughly predicted genes in the s. mansoni genome. in the merops database, there are currently known or putative proteases identified in s. mansoni. since over 90% of the genes presented here are new, this bioinformatic data mining represents a substantial expansion of putative proteases from this species. as expected, proteases of five catalytic classes were identified: 4% are aspartic, 26% are cysteine, 39% are metalloproteases, 24% are serine, and 6% are threonine proteases. these proportions are largely in harmony with those from other organisms. the recently published genome sequence of s. mansoni estimates the presence of protease sequences in families. for the protease families represented in both publications, estimated numbers are identical in families, and families are estimated by berriman et al. to have more members. in cases where estimates differ, most are very similar, the exception being families a c and s 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 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 residues or that overlapped less than 80% of the most similar homologue. comparatively, caenorhabditis elegans, a round worm with a well characterized and annotated genome, has known or putative proteases in the merops database. the proportions of classes of proteases are roughly equivalent, but we note a slight expansion in the relative proportion of serine proteases in c. elegans compared to s. mansoni, and a comparative expansion of cysteine proteases in s. mansoni. some differences will also naturally arise because of differences in organism complexity and life style. however, differences between these two species may also partially be attributable to the coverage and sequence quality of the genomes, and the fact that s. mansoni genome characterizations are newer and still very much subject to verification and basic delineation. most of the protein sequences that had high similarity to merops database sequences were verified as having a conserved protease-specific domain. kaas was able to assign orthology and kegg functional pathways to of the s. mansoni proteases. forty-one proteases are assigned to be involved in metabolic processes, while twenty-four are involved in genetic information processing. environmental information processes involve eleven proteases, while eleven additional proteases are engaged in cellular processes such as communication and cell cycling. we note that despite the removal of sequences that show similarity to inactive proteases in merops, and assignment of sequences to functional pathways, none of the new proteases identified in the present work have been experimentally shown to be catalytically active. 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. aspartic proteases eleven loci encoding aspartic proteases from just three families were identified. four of the aspartic proteases, all in the a family, were found to contain a signal peptide. transmembrane predictions differed between methods: tmhmm found three proteases with a tm domain, all in family a22; tups detected a total of tm domains among the a and a families. two loci were significantly similar to family a 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 a 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 is shared only among a m and s 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. the s. mansoni a protease smp_ contains both active site motifs, and in a phylogeny is closely associated with presenilin-type proteases from c. elegans. the conserved evolutionary function of presenilin proteases is the control of notch proteins, which act as regulators of gene expression and are involved in diverse cellular and tissue functions such as cell maturation, angiogenesis, and neuronal function and development. smp_ also contains both active site motifs, but forms part of a clade comprised of signal peptide proteases. the signal peptide proteases are not associated with notch signaling in c. elegans, but are involved in embryonic development and larval molting. impas protease knockout c. elegans have an embryonic lethal phenotype, possibly due to the function of the protease in lipid homeostasis and the production of cholesterol-derived hormones. thus it is significant that smp_ clusters with other signal peptide proteases, which are nonredundant and distinct from presenilin protease activity. the remaining a protease from s. mansoni, smp_ does not contain the complete catalytic dyad. smp_ is not allied closely in the phylogenetic tree with either presenilin or signal peptide proteases but the genetic distance shows it shares higher sequence similarity to smp_. interestingly, a family proteases cleave the signal peptides of mhc class i molecules in humans, which serve as a ligand for hla-e molecules. this activity reports successful mhc biosynthesis to the immune system and regulates nk cell mediated attack. cysteine proteases we detected 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. we detected members of the c 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 c 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. caspase proteases are also calcium-dependent, and are most prominently known to control apoptosis in a wide variety of animals, including other bilaterian worms. however, the so called inflammatory caspases mediate non-death functions such as inflammation, immunity, and maturation of a variety of cell types. although there is broad overlap, apoptosis caspases are often categorized as initiator, and effector caspases. the four s. mansoni caspases identified here all have the conserved catalytic motifs of his-gly and ala-cys, and are preceded by blocks of hydrophobic residues. c. elegans also has caspase loci, but only three have a conserved catalytic motif. in a sequence identity matrix of s. mansoni, c. elegans and human caspases, all of the s. mansoni caspases shared more similarity to caspases from humans rather than to any other species, including other s. mansoni caspases. in three out of the four cases, s. mansoni shared their highest similarity to human caspases, whereas all human caspases except one were most similar to another human caspase. caspases fall into three phylogenetic clades, which largely correspond with tetrapeptide substrate specificity. caspases from a species typically fall into multiple clades, with the known exception being c. elegans, whose caspases also form a species-specific clade in our phylogenetic analysis. s. mansoni caspases are dispersed among the three clades, as seen in most species, but unlike c. elegans. two s. mansoni caspases are in a clade with effector caspases from humans and mice, while smp_ is associated with classical initiators caspase and caspase the fourth trematode caspase is in a monophyletic group with the initiator caspase and a larger clade of mostly inflammatory caspases, which have a regulatory role in the immune system and are associated only with species having a complex hematopoesis involved in the immune response. the placement of s. mansoni caspases in the larger phylogeny raises interesting possibilities regarding the specificity and function of these proteases which warrants further investigation. although caspases are important regulatory proteins and are targets of chemotherapeutic agents in several pathologies, including cancer, no anti-schistosomal agents are currently being investigated that target these proteases. another group of important regulatory elements include the cysteine proteases that interact with ubiquitin, sumo and nedd molecules. 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. we have putatively identified more than members from the c c and c proteases families, which interact with ub-like protein molecules. these proteases are responsible for the activation and recycling 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 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. the bioinformatic approach found a locus that may correspond to the previously identified lap protease of family m. additionally, we found a putative locus for a previously isolated protein thought to be the smdppiii, in family m. 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 and the mitochondrial intermediate protease 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- subunits of the s. mansoni mpp. the β-mpp of s. mansoni has the conserved hxxehxe motif, indicating that it is probably catalytically active. 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. 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 cysteine residues, consistent with cysteine enrichment in the mip proteins of other species. 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 m family are detected in s. mansoni, and all contain an atp binding motif, but only one sequence 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. m 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 m family with an active site motif was detected in our analysis. this protease is predicted to have multiple transmembrane helices, and the putative active site is found within the third transmembrane helix, 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 s 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. serine proteases sixty serine proteases were detected in our screening of the s. mansoni predicted proteins, and these are divided among families. sixteen loci were found to have a predicted signal sequence--many of these are in the s family, which is consistent with the majority of known s 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 proteases with a tm alpha helix. 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. the s family is the largest group of proteases, with a wide variety of functions. this functional divergence is frequently reflected in phylogenetic grouping and/or variation at 5- base-pair motifs surrounding functionally important residues, such as active sites. we identified eighteen s proteases in the s. mansoni genome, however six of these did not have a significant similarity to a conserved protease domain. in addition, alignment of the sequences revealed that only seven of these predicted proteins have the conserved catalytic triad of his, asp, and ser. a phylogeny of s proteases from human, drosophila, c. elegans, and s. mansoni resulted in a general lack of resolution in the deeper nodes, making it difficult to ascertain any level of functional clustering. despite this, a strongly supported cluster of four s. mansoni proteases is formed among sequences with 58-99% identity. included in this cluster are cercarial elastase and other proteases of similar predicted length. two of the remaining s. mansoni s proteases are in a large unresolved polytomy that includes s proteases from all species included in the analysis. the final s. mansoni s protease is in a clade of "effector" proteases that function downstream in a signaling cascade and operate on cellular substrates. although it is impossible to assign functions to s. mansoni s proteases through the above analysis, results indicate a possible functional divergence among s. mansoni s proteases. some of these sequences may have a closely related function that is not shared with other organisms included in the analysis. we also found members of the s family that have a catalytic mechanism that is distinct from the typical chymotrypsin activity of s family proteases. this family is mostly comprised of endoproteases with broad function, many of which enter the secretory pathway. s. mansoni also has s 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 s 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 s 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. consistent with the expected function, these s proteases have several tm helices predicted by both tmhmm and tups, indicating a likely conserved structure among taxa. s family proteases are termed rhomboid proteases and can be divided into several groups because of conserved structure, substrate similarity, and cellular localization. these differences are reflected in their phylogenetic clustering into parl, secretase, and irhom-type proteases. we included putative s. mansoni rhomboid proteases in phylogenetic analysis to categorize these into subtypes and as an initial assessment of similarity and possible function. the resulting phylogenetic tree strongly supported groups corresponding to parl, secretase, and irhom proteases, but the relationships within and among the three groups were not always clear. the three s. mansoni putative rhomboid family members fell into three separate clades. smp_ has the conserved histidine and gxsx motif in a hydrophobic region predicted to be in a transmembrane helix. this is characteristic of proteolytically active rhomboids and smp_ was placed with the parl-like proteases, which localize to the mitochondria. smp_ clusters with the secretase-a rhomboids, and consistent with this clustering is the conserved catalytic motif in a hydrophobic region. smp_ is short and likely represents an incomplete sequence, but portions of it do show significant similarity to irhom-like rhomboids, including a conserved proline in the degenerate catalytic motif. irhoms lack a catalytic activity, but their phylogenetic clustering suggests some conserved functional relationship. these assessments of s. mansoni rhomboids to functional classes are simply based on similarity and await experimental confirmation. threonine proteases 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 alpha subunits and 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 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. 
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. 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 include calpains, caspases, cytosolic and mitochondrial signal peptidases, proteases that interact with ubiquitin and ubiquitin-like molecules, and proteases that perform regulated intramembrane proteolysis. to that end, we identified protease protein coding genes from the s. mansoni genome project and est library. we identified protease sequences from five catalytic classes using predicted proteins of the s. mansoni genome. 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. we characterized important regulatory proteases and focus analysis on these proteases to complement the growing knowledge base of digestive proteases. 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. the vast majority of these show significant similarity to proteins in kegg and the conserved domain database. 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. numerous proteases are identified for the first time in s. mansoni.
 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 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. 