Abstract
Ubiquitin-conjugating enzymes (Ub-E2) perform the second step of ubiquitination and, consequently, are essential for regulating proteolysis and for modulating protein function, interactions and trafficking. Previously, our group demonstrated the crucial role of ubiquitination and the Ub-proteasome pathway during the Schistosoma mansoni life cycle. In the present investigation, we used a homology-based genome-wide bioinformatics approach to identify and molecularly characterise the Ub-E2 enzymes in S. mansoni. The putative functions were further investigated through molecular phylogenetic and expression profile analyses using cercariae, adult worms, eggs and mechanically transformed schistosomula (MTS) cultured in vitro for 3.5 h or 1 or 3 days. We identified, via in silico analysis, 17 Ub-E2 enzymes with conserved structural characteristics: the beta-sheet and the helix-2 form a central core bordered by helix-1 at one side and helix-3 and helix-4 at the other. The observed quantitative differences in the steady-state transcript levels between the cercariae and adult worms may contribute to the differential protein ubiquitination observed during the parasite’s life cycle. This study is the first to identify and characterise the E2 ubiquitin conjugation family in S. mansoni and provides fundamental information regarding their molecular phylogenetics and developmental expression during intra-mammalian stages.
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References
Basch PF, DiConza JJ (1977) In vitro development of Schistosoma mansoni cercariae. J Parasitol 63:245–249
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. doi:10.1093/nar/gku340
Burroughs AM, Jaffee M, Iyer LM, Aravind L (2008) Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J Struct Biol 162:205–218. doi:10.1016/j.jsb.2007.12.006
Castro-Borges W, Cartwright J, Ashton PD, Braschi S, Guerra Sa R, Rodrigues V, Wilson RA, Curwen RS (2007) The 20S proteasome of Schistosoma mansoni: a proteomic analysis. Proteomics 7:1065–1075. doi:10.1002/pmic.200600166
Cottee PA, Abs ELOYG, Nisbet AJ, Gasser RB (2006) Ubiquitin-conjugating enzyme genes in Oesophagostomum dentatum. Parasitol Res 99:119–125. doi:10.1007/s00436-005-0111-x
David Y, Ziv T, Admon A, Navon A (2010) The E2 ubiquitin-conjugating enzymes direct polyubiquitination to preferred lysines. J Biol Chem 285:8595–8604. doi:10.1074/jbc.M109.089003
Garnett MJ, Mansfeld J, Godwin C, Matsusaka T, Wu J, Russell P, Pines J, Venkitaraman AR (2009) UBE2S elongates ubiquitin chains on APC/C substrates to promote mitotic exit. Nat Cell Biol 11:1363–1369. doi:10.1038/ncb1983
Guerra-Sa R, Castro-Borges W, Evangelista EA, Kettelhut IC, Rodrigues V (2005) Schistosoma mansoni: functional proteasomes are required for development in the vertebrate host. Exp Parasitol 109:228–236. doi:10.1016/j.exppara.2005.01.002
Haas AL, Siepmann TJ (1997) Pathways of ubiquitin conjugation. FASEB J 11:1257–1268
Haddad DM, Vilain S, Vos M, Esposito G, Matta S, Kalscheuer VM, Craessaerts K, Leyssen M, Nascimento RM, Vianna-Morgante AM, De Strooper B, Van Esch H, Morais VA, Verstreken P (2013) Mutations in the intellectual disability gene Ube2a cause neuronal dysfunction and impair parkin-dependent mitophagy. Mol Cell 50:831–843. doi:10.1016/j.molcel.2013.04.012
Harrop R, Wilson RA (1993) Protein synthesis and release by cultured schistosomula of Schistosoma mansoni. Parasitology 107:265–274. doi:10.1017/S0031182000079245
Jones D, Crowe E, Stevens TA, Candido EP (2002) Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins. Genome Biol. doi:10.1186/gb-2001-3-1-research0002
Kaiser P, Huang L (2005) Global approaches to understanding ubiquitination. Genome Biol 6:233. doi:10.1186/gb-2005-6-10-233
Komander D, Rape M (2012) The ubiquitin code. Annu Rev Biochem 81:203–229. doi:10.1146/annurev-biochem-060310-170328
Lenk U, Yu H, Walter J, Gelman MS, Hartmann E, Kopito RR, Sommer T (2002) A role for mammalian Ubc6 homologues in ER-associated protein degradation. J Cell Sci 115:3007–3014
Liu Y, Ye Y (2011) Proteostasis regulation at the endoplasmic reticulum: a new perturbation site for targeted cancer therapy. Cell Res 21:867–883. doi:10.1038/cr.2011.75
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods 25:402–408
Pereira RV, Cabral FJ, Gomes MS, Baba EH, Jannotti-Passos LK, Carvalho O, Rodrigues V, Afonso RJ, Castro-Borges W, Guerra-Sa R (2011) Molecular characterization of SUMO E2 conjugation enzyme: differential expression profile in Schistosoma mansoni. Parasitol Res 109:1537–1546. doi:10.1007/s00436-011-2394-4
Pereira RV, Gomes Mde S, Olmo RP, Souza DM, Jannotti-Passos LK, Baba EH, Castro-Borges W, Guerra-Sa R (2013) NEDD8 conjugation in Schistosoma mansoni: genome analysis and expression profiles. Parasitol Int 62:199–207. doi:10.1016/j.parint.2012.12.009
Pereira RV, Vieira HG, de Oliveira VF, Gomes Mde S, Passos LK, Borges Wde C, Guerra-Sa R (2014) Conservation and developmental expression of ubiquitin isopeptidases in Schistosoma mansoni. Mem Inst Oswaldo Cruz 109:1–8. doi:10.1590/0074-0276130107
Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8:785–786. doi:10.1038/nmeth.1701
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Summers MK, Pan B, Mukhyala K, Jackson PK (2008) The unique N terminus of the UbcH10 E2 enzyme controls the threshold for APC activation and enhances checkpoint regulation of the APC. Mol Cell 31:544–556. doi:10.1016/j.molcel.2008.07.014
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121
van Ree JH, Jeganathan KB, Malureanu L, van Deursen JM (2010) Overexpression of the E2 ubiquitin-conjugating enzyme UbcH10 causes chromosome missegregation and tumor formation. J Cell Biol 188:83–100. doi:10.1083/jcb.200906147
van Wijk SJ, Timmers HT (2010) The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins. FASEB J 24:981–993. doi:10.1096/fj.09-136259
Wu T, Merbl Y, Huo Y, Gallop JL, Tzur A, Kirschner MW (2010) UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex. Proc Natl Acad Sci U S A 107:1355–1360. doi:10.1073/pnas.0912802107
Ye Y, Rape M (2009) Building ubiquitin chains: E2 enzymes at work. Nat Rev Mol Cell Biol 10:755–764. doi:10.1038/nrm2780
Acknowledgments
The authors thank the following transcriptome initiatives: São Paulo Transcriptome Consortium; Minas Gerais Genome Network and Wellcome Trust Genome Initiative (UK). This work was supported by the following Brazilian research agencies: FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais, CBB02101/11), NUBIO/UFOP and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico).
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Costa, M.P., Oliveira, V.F., Pereira, R.V. et al. In silico analysis and developmental expression of ubiquitin-conjugating enzymes in Schistosoma mansoni . Parasitol Res 114, 1769–1777 (2015). https://doi.org/10.1007/s00436-015-4362-x
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DOI: https://doi.org/10.1007/s00436-015-4362-x