Introduction

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) was originally identified in Arabidopsis mutants that mimic the phenotype of light-grown seedlings when grown in the dark (Wei and Deng 1992). CSN has also been identified in all eukaryotic cells studied, including Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens (Wee et al. 2002; Maytal-Kivity et al. 2003; Mundt et al. 1999; Busch et al. 2003; Pintard et al. 2003; Freilich et al. 1999; Henke et al. 1999). CSN is a highly conserved protein complex that consists of eight subunits known as CSN1 to CSN8 in higher eukaryotes (reviewed in Wei and Deng 2003). CSN controls the DNA damage response, cell cycle regulation, gene expression and the ubiquitin–proteasome system (UPS). Thus, this complex is involved in various cellular processes, including light regulation, inflammation, hormone signalling, oxygen homeostasis and tumour growth (Wei et al. 2008).

The CSN subunits have a counterpart in the ‘lid’ of the 26S proteasome (Li and Deng 2003), suggesting a common evolutionary origin and possibly, a related biochemical function (reviewed in Pick et al. 2009). CSN and the 26S proteasome ‘lid’ are each composed of eight proteins that have been labelled in six proteasome, COP9 signalosome and initiation factor eIF3 (PCI) domain subunit proteins (Dessau et al. 2008; Fu et al. 2001) and two MOV34 and Pad1 N-terminal (MPN) domain subunit proteins (Maytal-Kivity et al. 2002). The MPN domain proteins have primarily been associated with the deneddylation activity of the CSN and the deubiquitylation activity of the 26S proteasome, being subdivided into the biochemically active MPN+ domain subunit (CSN5) and the inactive MPN domain subunit (CSN6) (Maytal-Kivity et al. 2002). The PCI domain is thought to mediate interactions between individual subunits within the respective protein complexes (Dessau et al. 2008; Fu et al. 2001).

CSN has a central role in the UPS, as it mediates the degradation of proteins, typically those proteins with a regulatory function (Wei et al. 2008). Proteins destined for proteasomal degradation are first recognised by E3 ubiquitin ligases, subsequently polyubiquitylated by E2 ubiquitin-conjugating enzymes and then—in their polyubiquitylated form—bound and degraded by the 26S proteasome (reviewed in Bhat and Greer 2011). Thus, members of the E3 ubiquitin ligase family provide an important point of ubiquitination regulation. The combinatorial organisation of E3 ubiquitin ligases, specifically the cullin-RING E3 ubiquitin ligase (CRL) family, is formed by the interactions of an E3 core complex, which consists of a cullin subunit, RBX1/ROC1, with a cullin-specific adaptor and substrate recognition subunit (reviewed in Merlet et al. 2009).

In Schistosoma mansoni, the UPS has been studied in cercariae, lung-worms, adults and eggs (Mathieson et al. 2011; Nabhan et al. 2007; Guerra-Sá et al. 2005). In Mus musculus, proteasome inhibitors prevent larval development and reduce adult worm burden (Guerra-Sá et al. 2005). The UPS has been implicated not only in degrading vitelline cells, but also more during the development of the envelope than in the miracidium (Mathieson et al. 2011). In addition, separation of the 20S proteasome obtained from adult worms into 58 spots by 2D gel analysis suggests that the alpha and beta subunits were extensively post-translationally modified at different intensities between cercariae and adult worms (Castro-Borges et al. 2007). These observations suggest that post-translation modifications, i.e., phosphorylation, directly affect the interactions of 20S with its natural regulators, such as PA700, PA28 and CSN.

In this work, we characterised the S. mansoni UPS regulators by examining the CSN complex. The predicted proteins involved in this complex were conserved when searching the parasite databases. Furthermore, the gene expression of all CSN subunits was evaluated by quantitative (q)RT-PCR at different stages of the S. mansoni life cycle using cercariae, adult worms and mechanically transformed schistosomula (MTS). These gene expression profiles suggested essential roles of the CSN complex in parasite development.

Materials and methods

Ethics statement

All experiments were authorised by the Ethical Committee for Animal Care of the University of Ouro Preto and were performed in accordance with the national and international regulations accepted for laboratory animal use and care.

Parasites

The S. mansoni parasite (LE strain) was maintained by routine passage through Biomphalaria glabrata snails and BALB/c mice. The infected snails were induced to shed cercariae under light exposure for 2 h and the cercariae were recovered by sedimentation on ice. Adult worm parasites were obtained by liver perfusion of mice after 50 days of infection. The MTS were prepared as described by Harrop and Wilson (1993). Briefly, cercariae were recovered, washed in RPMI 1640 medium (Invitrogen, São Paulo, Brazil), vortexed at maximum speed for 90 s and immediately cultured for 3.5 h at 37 °C in a 5 % CO2 incubator. Then, the recovered schistosomula were washed with RPMI 1640 until no tails were detected. For subsequent incubations, the parasites were maintained in M169 medium supplemented with 10 % foetal bovine serum), penicillin (100 μg/mL), streptomycin (100 μg/mL) and 5 % of Schneider’s medium (Basch and DiConza 1977) at 37 °C in a 5 % CO2 incubator for 3.5 h, 1, 2, 3, 5 and 7 days.

Computational analysis of CSN

Amino acid sequences of the CSN subunits were searched through the S. mansoni genome database version 5.0 from GeneDB (http://www.genedb.org/genedb/smansoni/) using orthologues from D. melanogaster, C. elegans and H. sapiens as queries. The BLASTp algorithm, underpinned by the PFAM (v 26.0) database, was used for searches of conserved protein domains or motifs from S. mansoni sequences.

Multiple alignments of SmCSN1, SmCSN2, SmCSN3, SmCSN4, SmCSN5, SmCSN6, SmCSN7 and SmCSN8 were performed using BLAST. The evolutionary history was inferred using the Neighbour-Joining method (Saitou and Nei 1987). The bootstrap consensus tree inferred from 1,000 replicates represents the evolutionary history of the taxa analysed (Felsenstein 1985). Branches corresponding to partitions reproduced in less than 50 % bootstrap replicates are collapsed. The tree is drawn to scale, with the same units used for both branch length and the evolutionary distances used to infer the phylogenetic tree. Branches with bootstrap values lower than 30 were hidden. The evolutionary distances were computed using the JTT matrix-based method (Jones et al. 1992) and are in the units of the number of amino acid substitutions per site. The analysis involved 77 amino acid sequences, and all positions containing gaps and missing data were eliminated. The evolutionary analyses were conducted in MEGA 5 (Tamura et al. 2011).

Expression analysis of CSN components

Total RNA was extracted from cercariae, schistosomula and adult worms using a combination of the TRIzol reagent (Gibco-BRL) and chloroform. The RNA was then column purified using the SV Total RNA Isolation System (Promega, Belo Horizonte, Brazil). The preparation was treated with RNase-free DNase I in three different rounds with decreasing enzyme concentrations (RQ1 DNase; Promega). RNA was quantified using a spectrophotometer and an aliquot containing 1 μg of total RNA reverse transcribed using an oligo(dT) primer from the ThermoScript RT-PCR System (Invitrogen São Paulo, Brazil) as described by the manufacturer. The efficiency of DNase I treatment was evaluated by PCR amplification of the cDNA reaction mix without the addition of the ThermoScript enzyme. S. mansoni-specific primers were designed using GeneRunner® software. The sequence accession numbers and their primer pairs are listed in a supplementary table (Table S1). Reverse-transcribed cDNA samples were used as templates for PCR amplification using SYBR Green Master Mix UDG-ROX® (Invitrogen) and a 7300 Real Time PCR System (Applied Biosystems, Rio de Janeiro, Brazil). Specific primers for S. mansoni EIF4E were used as an endogenous control (GeneDB ID: Smp_001500) (forward 5′TGTTCCAACCACGGTCTCG3′, reverse 5′TCGCCTTCCAATGCTTAGG3′) (Liu et al. 2012). The efficiency of each pair of primers was evaluated according to the protocol developed by Applied Biosystems (cDNA dilutions were 1:10, 1:100 and 1:1000). For all transcripts investigated, three biological replicates were performed and gene expression was normalised against the EIF4E transcript according to the 2−ΔCt method (Livak and Schmittgen 2001) using the Applied Biosystems 7300 software.

Statistical analysis

Statistical analyses were performed using the GraphPad Prism version 5.0 software (Irvine, CA, USA). Data were normalised using one-way analysis of variance. Tukey’s post-hoc test was used to investigate significant differential expression of transcripts throughout the investigated stages. The differences were considered significant when p values were <0.05.

Results

CSN in S. mansoni: organisation and intrinsic function

To obtain more detailed information about CSN members, we undertook a series of orthologue analyses. These included multiple sequence alignments to identify putative conserved motifs of schistosome orthologues and construct phylogenetic trees to place novel schistosome genes accurately within the appropriate family. This analysis identified eight putative proteins involved in the CSN complex in S. mansoni, i.e., SmCSN1 (Smp_138920.1), SmCSN2 (Smp_020050), SmCSN3 (Smp_164800), SmCSN4 (Smp_085640), SmCSN5 (Smp_131660), SmCSN6 (Smp_126690), SmCSN7 (Smp_212230) and SmCSN8 (Smp_025680). The conserved domains of these subunits were then assigned. The subunits CSN1, 2, 3, 4 and 7 are relatively similar in size and contain a PCI domain (Pfam number: PF01399) in the C-terminus and the CSN8 subunit has a characteristic PCI domain (Pfam number: PF10075). The CSN5 and 6 subunits have an MPN domain (Pfam number: PF01398) and are JAB1/MPN/MOV34 metalloenzyme (JAMM) metalloproteases, which trigger the cleavage of the ubiquitin-related Nedd8/Rub1 from CSN target proteins, a process known as deneddylation. Consistent with its function, CSN5 displays homology to the RNN11, a subunit of the 26S proteasome ‘lid’ that cleaves ubiquitin from proteins.

S. mansoni CSN subunits and their orthologues from H. sapiens and Schistosoma japonicum are presented in Table 1. In humans, there is a subunit 7 isoform, which was not observed in S. mansoni or S. japonicum. Comparing the S. mansoni human CSN subunits, CSN8 was least conserved among them, displaying 25 % identity and CSN2 was the most conserved, with 72 % identity. Comparing SmCSN subunits to those of S. japonicum, all subunits were well conserved (>69 %). Recent reports have shown that the MPN domain is the most conserved (reviewed in Chamovitz 2009; Wei et al. 2008).

Table 1 COP9 signalosome subunits of S. mansoni and their orthologs in H. sapiens and S. japonicum
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The phylogenetic analysis generated using these proteins (Fig. 1) revealed homology among orthologues, suggesting conserved assembly mechanisms for the complex. Our results demonstrated that the S. mansoni genes were similar to those found in protostomes, such as C. elegans and D. melanogaster, and identical to S. japonicum, reinforcing the conservation of the CSN complex.

Fig. 1
figure 1

Phylogenetic tree of S. mansoni CSN subunits. Conservation of SmCSN1, SmCSN2, SmCSN3, SmCSN4, SmCSN5, SmCSN6, SmCSN7 and SmCSN8. Multiple alignments were performed using Mega 5.0 with bootstrap analysis. Bootstrap percentages are indicated at each branch

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Structural aspects of CSN and 26S proteasome ‘lid’

To elucidate the potential function of the CSN complex in S. mansoni, we analysed the presence of significant sequence homologies of the CSN and 26S proteasome ‘lid’ subunits to determine common architecture for the two complexes (Table 2). Comparing the S. mansoni and human CSN subunits, we found that CSN1 and RPN7 are paralogues but less conserved among the other subunits, showing 25 % identity, whereas CSN5 and RPN11 were more highly conserved with 80 % identity, sharing PCI and MPN domains, respectively.

Table 2 Subunit comparisons among S. mansoni CSN subunits and proteasome lid paralogues
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The phylogenetic tree showed conservation among the subunits, which also confirmed the gene duplication of these paralogues in S. mansoni (Fig. 2). Notably, the nomenclature used to designate the CSN and 26S proteasome ‘lid’ subunits was standardised by Deng et al. (2000) and Finley et al. (1998), respectively.

Fig. 2
figure 2

Phylogenetic tree of S. mansoni CSN subunits and their paralogous SmRPNs. Gene duplication among SmCNs and SmRPNs was confirmed. Multiple alignments were performed using Mega 5.0 with bootstrap analysis. Bootstrap percentages are indicated at each branch

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Differential profile of CSN subunits in schistosome life cycle

We used real time PCR to quantify the mRNA expression levels of the CSN subunits in several developmental stages of the schistosome life cycle. Three techniques were performed and three biological replicates were used. The relative expression levels of Smcsn1, Smcsn2, Smcsn3, Smcsn4, Smcsn5, Smcsn6, Smcsn7 and Smcsn8 were analysed using RNA levels in relation to the constitutively expressed gene EIF4E (Fig. 3). We observed that all CSN subunits were expressed at all developmental stages analysed, but curiously, each subunit has a typical expression profile. Furthermore, all CSN subunits were up-regulated in the adult worm compared to the cercariae stage (Fig. 3a). During schistosomula development, no relevant changes in the expression profile were observed (Figs. 3b, c d,).

Fig. 3
figure 3

Similar expression of CSN subunits throughout the S. mansoni life cycle. The SmCSN1, SmCSN2, SmCSN3, SmCSN4, SmCSN5, SmCSN6, SmCSN7 and SmCSN8 mRNA expression levels were measured, based on three replicates, in the cercariae (MTS-3.5 h and 1, 2, 3, 5 and 7 days) and adult worm stages using quantitative RT-PCR. Expression levels were calibrated according to the comparative 2−ΔCt method, using the constitutively expressed SmEIF4E gene as an endogenous control (one-way variance analysis followed by Tukey pairwise comparison, p < 0.05). Single asterisk, different from CSN1; double asterisk, different from CSN2; triple asterisk, different from CSN3; single number sign, different from CSN4; double number sign, different from CSN5; triple number sign, different from CSN6 and different from CSN7

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Discussion

Here, we demonstrate that S. mansoni CSN has eight conserved subunits: CSN1, 2, 3, 4, 5, 6, 7 and 8. Furthermore, five subunits, CSN1, 2, 3, 4 and 7, contain a ‘typical’ PCI domain (Pfam number: PF01399), CSN8 shares an ‘atypical’ PCI domain (Pfam number: PF10075) and CSN5-6 contain the JAMM/MPN domain (Pfam number: PF01398) (Pick et al. 2009). CSN is considered an evolutionarily conserved, multifunctional complex found in eukaryotes (reviewed in Wei and Deng 2003). The CSN subunits can be divided into two groups: CSN1, 2, 3, 4, 7 and 8, which contain the motif that mediates the PCI-specific protein interactions necessary for the integrity of the complex and CSN5 and 6, which participate in the deneddylation activity of the complex. Although CSN6 also has a JAMM/MPN domain, it lacks a zinc binding domain and catalytic activity (Maytal-Kivity et al. 2002). The CSN complex is organised in two modules, CSN1/2/3/8 and CSN4/5/6/7, and connected by interactions between CSN1 and CSN6 (Sharon et al. 2009). Although the precise molecular mechanisms need further investigation, at least one of the physiological roles of the CSN may lie in its involvement in the protein life cycle from synthesis to degradation.

The conservation of CSN subunits was confirmed by the high homology of eight subunits when compared with those of humans and S. japonicum. This result was supported by construction of a phylogenetic tree, suggesting conservation of both function and assembly of the CSN complex. In addition, CSN has high homology to the 26S proteasome ‘lid’; thus, the CSN subunits are considered paralogues of the eight proteasome lid subunits. Therefore, one possible function of the CSN is as an alternative lid for the proteasome (Mikus and Zundel 2005). We demonstrated the homology and conservation among paralogues by phylogenetic analysis. The similarity in the composition of subunits suggested that these two complexes originated from a common ancestor and share similar molecular properties.

Currently, the exact function of the CSN complex remains undefined, although it clearly plays a role in protein stability within the UPS. CSN is involved in regulating cullin-based E3 ligases (CRLs) because the modification of Nedd8 is required for the activation of CRLs (Ohh et al. 2002). The down-regulation of CSN was originally postulated to up-regulate CRL activity by increasing levels of neddylated cullins. However, experimental results showed that the CSN is actually required for the activation of CRLs (reviewed in Merlet et al. 2009; Pintard et al. 2003; Wang et al. 2003). This activity can regulate transcription factor stability and therefore transcriptional activity. Recent data have suggested that the CSN also regulates transcription at the chromatin level by mechanisms that are not yet fully understood. Furthermore, the CSN subunits CSN5 and CSN2 seem to act as transcriptional co-activators and co-repressors, respectively (reviewed in Chamovitz 2009).

The mRNA expression results suggest that all the subunits are important for the assembly of the complex. In a recent study in Neurospora crassa, those subunits have been individually characterised and are related to the regulation of cullin protein deneddylation and stability. Knockout mutants have been made for each subunit of the CSN, except the CSN3 subunit, which was lethal. All other mutants have showed severe defects during development, indicating that those subunits are required for stability of Cul1 in SCF complexes and Cul3 and BTB proteins in Cul3-BTB E3s (Wang et al. 2010). Furthermore, deregulation of CSN subunit function can have a dramatic effect on diverse cellular functions, including the maintenance of DNA fidelity, cell cycle control, DNA repair, angiogenesis, and micro environmental homeostasis (Richardson and Zundel 2005).

Among the eight CSN subunits, CSN5 and 6 contain a MPN domain, but CSN5 harbours a very specific JAMM motif, which is conserved and plays a critical role among the different metalloproteases. In the case of RPN11, this activity is used to remove ubiquitin from the substrate before degradation by the 26S proteasome (Verma et al. 2002). However, the lone CSN5 polypeptide does not exhibit metalloprotease activity (Cope et al. 2002), suggesting that another CSN component, most likely the CSN holocomplex, is required for the deneddylase activity (Sharon et al. 2009). Furthermore, CSN5 is not necessary for the integrity of the complex, although this subunit was found to confer additional stability to CSN (Sharon et al. 2009; Tomoda et al. 2002).

In the present work, our data showed that CSN is up-regulated in adult worms and down-regulated in cercariae, suggesting that CSN also functions as a ‘lid’ alternative to the 20S proteasome in S. mansoni. However, the expression levels of each subunit are not similar in all stages of development; these subunits are likely under the control of different promoters because they are located on different chromosomes. Furthermore, recent data indicate that multiple CSN-independent forms can be found in complexes of lower molecular mass than the intact complex (mini-CSNs) (Mundt et al. 2002; Oron et al. 2002). In addition, previous studies have shown that CSN1, CSN2, and CSN8 are associated with the holocomplex under normal conditions and are predominantly nuclear-localised (Tomoda et al. 2002; Wei and Deng 1998; Chamovitz et al. 1996). CSN-independent CSN5 is found in both the nucleus and cytoplasm. Dependence of CSN5 nuclear accumulation on other subunits has been demonstrated in the budding yeast CSN-like complex (Maytal-Kivity et al. 2003; Bounpheng et al. 2000). Furthermore, the mini-CSN complex containing CSN5 and a subset of other CSN subunits is mostly cytosolic (Tomoda et al. 2002). The higher mRNA levels may reflect for the participation of these proteins in other unidentified functions outside the CSN and merit further examination.

The differential expression of complex subunits has also been observed for S. mansoni proteasome subunits (Nabhan et al. 2007). In this study, a total of 31 putative proteasomal subunits were identified, including 17 19S (regulatory particle) subunits and 14 20S (catalytic core) subunits. The examination of S. mansoni proteasome subunit expression levels by qRT-PCR revealed that the proteasome components were differentially expressed among cercariae, schistosomula, and adult worms. In particular, the data suggest that the proteasome may be down-regulated during the early stages of schistosomula development and is subsequently up-regulated as the parasite matures to the adult stage, confirming the involvement of the proteasome in parasite development and survival.

The first evidence suggesting the importance of the proteasome during S. mansoni development was provided by Guerra-Sá et al. (2005). During experimental schistosomiasis, proteasome inhibitors were able to reduce the number of lung stage schistosomula and thus the worm burden, which consequently decreased the egg output in infected mice. These results support the hypothesis that this particular degradation pathway is an important determinant for the successful development of cercariae in the vertebrate host (Guerra-Sá et al. 2005).

Furthermore, Castro-Borges et al. (2007) observed changes in the proteasome structure, likely caused by the introduction of a new set of posttranslational modifications (PTMs), during the transformation of the cercariae to the skin schistosomula stage. Additionally, modifying the α-subunits was reported to allow different binding capabilities for regulatory particles, thus altering which substrates could be degraded (Glickman and Raveh 2005). Taken together, these reports suggest that the range of PTMs, yet to be characterised, may reflect variations in proteasome function in different parasite tissues (Castro-Borges et al. 2007). Moreover, these results confirm the importance of proteasome plasticity because in this period, no cell division takes place until the invading parasite has completed its migration from the skin to the portal system and begun to feed on blood (Lawson and Wilson 1980).

In addition, Pereira-Júnior et al. (2013) reported 3.5 times lower expression of six 19S ATPase subunits of cercariae compared to adult worms. However, Nabhan et al. (2007) showed a relatively higher expression level of some 19S non-ATPase subunits (RNP1 and RPN10) in cercariae compared to adult worms. Furthermore, although the levels of 20S proteasome were not significantly lower when comparing cercariae and adult worms, the UPS activity is 16 times higher in cercariae, which supports the hypothesis those high levels of ‘lid’ subunits interfere with the amount of functional 26S subunit. This hypothesis is also supported by the accumulation of ubiquitinated substrate observed in cercariae (Guerra-Sá et al. 2005), indicating that during the life cycle of the parasite, different populations of proteasomes and their natural regulators coexist. Therefore, comparative studies between neddylation and ubiquitination are necessary to confirm this hypothesis. More in-depth genomic and proteomic analyses will be needed to determine the identification of the mechanism(s) involved in the regulation of CSN subunits and the involvement of CSN in the regulation of S. mansoni development.