Transcriptome and venom proteome of the box jellyfish Chironex fleckeri

BMC Genomics

Jason Mulvenna³  David Kvaskoff⁵  Debasis Dash¹  Dhirendra Kumar¹  Jeremy Potriquet⁴  Xinying Jia⁴  Diane L Brinkman² 

[1] G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India;Australian Institute of Marine Science, Townsville, QLD, Australia;The University of Queensland, School of Biomedical Sciences, Brisbane, QLD, Australia;Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia;The University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, Brisbane, QLD, Australia

关键词: Proteome;    Transcriptome;    Venom;    Chironex fleckeri;   

Others  :  1208972
DOI  :  10.1186/s12864-015-1568-3

 received in 2014-11-02, accepted in 2015-04-23,  发布年份 2015

【 摘 要 】

Background

The box jellyfish, Chironex fleckeri, is the largest and most dangerous cubozoan jellyfish to humans. It produces potent and rapid-acting venom and its sting causes severe localized and systemic effects that are potentially life-threatening. In this study, a combined transcriptomic and proteomic approach was used to identify C. fleckeri proteins that elicit toxic effects in envenoming.

Results

More than 40,000,000 Illumina reads were used to de novo assemble ∼ 34,000 contiguous cDNA sequences and ∼ 20,000 proteins were predicted based on homology searches, protein motifs, gene ontology and biological pathway mapping. More than 170 potential toxin proteins were identified from the transcriptome on the basis of homology to known toxins in publicly available sequence databases. MS/MS analysis of C. fleckeri venom identified over 250 proteins, including a subset of the toxins predicted from analysis of the transcriptome. Potential toxins identified using MS/MS included metalloproteinases, an alpha-macroglobulin domain containing protein, two CRISP proteins and a turripeptide-like protease inhibitor. Nine novel examples of a taxonomically restricted family of potent cnidarian pore-forming toxins were also identified. Members of this toxin family are potently haemolytic and cause pain, inflammation, dermonecrosis, cardiovascular collapse and death in experimental animals, suggesting that these toxins are responsible for many of the symptoms of C. fleckeri envenomation.

Conclusions

This study provides the first overview of a box jellyfish transcriptome which, coupled with venom proteomics data, enhances our current understanding of box jellyfish venom composition and the molecular structure and function of cnidarian toxins. The generated data represent a useful resource to guide future comparative studies, novel protein/peptide discovery and the development of more effective treatments for jellyfish stings in humans. (Length: 300).

【 授权许可】

   
2015 Brinkman et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Brinkman DL, Burnell JN. Biochemical and molecular characterisation of cubozoan protein toxins. Toxicon. 2009; 54:1162-73.
• [2]Brinkman DL, Konstantakopoulos N, McInerney BV, Mulvenna J, Seymour JE, Isbister GK et al.. Chironex fleckeri (box jellyfish) venom proteins: Expansion of a cnidarian toxin family that elicits variable cytolytic and cardiovascular effects. J Biol Chem. 2014; 289:4798-812.
• [3]Chaousis S, Smout M, Wilson D, Loukas A, Mulvenna J, Seymour J. Rapid short term and gradual permanent cardiotoxic effects of vertebrate toxins from Chironex fleckeri (Australian box jellyfish) venom. Toxicon. 2014; 80:17-26.
• [4]Hughes RJ, Angus JA, Winkel KD, Wright CE. A pharmacological investigation of the venom extract of the australian box jellyfish, Chironex fleckeri, in cardiac and vascular tissues. Toxicol Lett. 2012; 209:11-20.
• [5]Yanagihara AA, Shohet RV. Cubozoan venom-induced cardiovascular collapse is caused by hyperkalemia and prevented by zinc gluconate in mice. PLoS ONE. 2012; 7:e51368.
• [6]Brinkman DL, Aziz A, Loukas A, Potriquet J, Seymour J, Mulvenna J. Venom proteome of the box jellyfish Chironex fleckeri. PLoS ONE. 2012; 7:e47866.
• [7]Laha T, Pinlaor P, Mulvenna J, Sripa B, Sripa M, Smout MJ et al.. Gene discovery for the carcinogenic human liver fluke, opisthorchis viverrini. BMC Genomics. 2007; 8:189. BioMed Central Full Text
• [8]Cantacessi C, Mulvenna J, Young ND, Kasny M, Horak P, Aziz A et al.. A deep exploration of the transcriptome and "excretory/secretory" proteome of adult Fascioloides magna. Mol Cell Proteomics. 2012; 11:1340-53.
• [9]Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012; 28:1086-92.
• [10]Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007; 23:1061-7.
• [11]Zdobnov EM, Apweiler R. InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001; 17:847-8.
• [12]Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011; 8:785-6.
• [13]Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305:567-80.
• [14]Jungo F, Bougueleret L, Xenarios I, Poux S. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. Toxicon. 2012; 60:551-7.
• [15]Trevisan-Silva D, Gremski LH, Chaim OM, da Silveira RB, Meissner GO, Mangili OC et al.. Astacin-like metalloproteases are a gene family of toxins present in the venom of different species of the brown spider (genus Loxosceles). Biochimie. 2010; 92:21-32.
• [16]Rehana S, Manjunatha Kini R. Molecular isoforms of cobra venom factor-like proteins in the venom of Austrelaps superbus. Toxicon. 2007; 50:32-52.
• [17]Le Minh TN, Reza MA, Swarup S, Kini RM. Gene duplication of coagulation factor V and origin of venom prothrombin activator in Pseudonaja textilis snake. Thromb Haemost. 2005; 93:420-9.
• [18]Brinkman D, Burnell J. Identification, cloning and sequencing of two major venom proteins from the box jellyfish. Chironex fleckeri. Toxicon. 2007; 50:850-60.
• [19]Nagai H, Takuwa K, Nakao M, Ito E, Miyake M, Noda M et al.. Novel proteinaceous toxins from the box jellyfish (sea wasp) Carybdea rastoni. Biochem Biophys Res Commun. 2000; 275:582-8.
• [20]Nagai H, Takuwa K, Nakao M, Sakamoto B, Crow GL, Nakajima T. Isolation and characterization of a novel protein toxin from the Hawaiian box jellyfish (sea wasp) Carybdea alata. Biochem Biophys Res Commun. 2000; 275:589-94.
• [21]Nagai H, Takuwa-Kuroda K, Nakao M, Oshiro N, Iwanaga S, Nakajima T. A novel protein toxin from the deadly box jellyfish (sea wasp, Habu-kurage) Chiropsalmus quadrigatus. Biosci Biotech Bioch. 2002; 66:97-102.
• [22]Ávila Soria, G. Molecular characterization of Carukia barnesi and Malo kingi, Cnidaria; Cubozoa; Carybdeidae. Ph.D. thesis, James Cook University. 2009.
• [23]Brinkman D, Burnell J. Partial purification of cytolytic venom proteins from the box jellyfish. Chironex fleckeri. Toxicon. 2008; 51:853-63.
• [24]Endean TR, Rifkin J. Isolation of different types of nematocyst from the cubomedusan Chironex fleckeri. Toxicon. 1975; 13:375-6.
• [25]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I et al.. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29:644-52.
• [26]Horton P, Park K, Obayashi T, Fujita N, Harada H, Adams-Collier CJ et al.. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007; 35:W585-7.
• [27]Rachamim T, Morgenstern D, Aharonovich D, Brekhman V, Lotan T, Sher D. The dynamically evolving nematocyst content of an anthozoan, a scyphozoan, and a hydrozoan. Mol Biol Evol. 2015; 32:740-53.
• [28]Fry BG, Roelants K, Champagne DE, Scheib H, Tyndall JD, King GF et al.. The toxicogenomic multiverse: convergent recruitment of proteins into animal venoms. Annu Rev Genomics Hum Genet. 2009; 10:483-511.
• [29]Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. 2013; 14:328. BioMed Central Full Text
• [30]Li R, Yu H, Xue W, Yue Y, Liu S, Xing R et al.. Jellyfish venomics and venom gland transcriptomics analysis of Stomolophus meleagris to reveal the toxins associated with sting. J Proteomics. 2014; 106C:17-29.
• [31]Lassen S, Helmholz H, Ruhnau C, Prange A. A novel proteinaceous cytotoxin from the northern Scyphozoa Cyanea capillata (L.) with structural homology to cubozoan haemolysins. Toxicon. 2011; 57:721-9.
• [32]Weston AJ, Chung R, Dunlap WC, Morandini AC, Marques AC, Moura-da Silva AM et al.. Proteomic characterisation of toxins isolated from nematocysts of the South Atlantic jellyfish Olindias sambaquiensis. Toxicon. 2013; 71:11-7.
• [33]Möhrlen F, Maniura M, Plickert G, Frohme M, Frank U. Evolution of astacin-like metalloproteases in animals and their function in development. Evol Dev. 2006; 8:223-31.
• [34]Pan T, Gröger H, Schmid V, Spring J. A toxin homology domain in an astacin-like metalloproteinase of the jellyfish Podocoryne carnea with a dual role in digestion and development. Dev Genes Evol. 1998; 208:259-66.
• [35]Calvete JJ, Fasoli E, Sanz L, Boschetti E, Righetti PG. Exploring the venom proteome of the western diamondback rattlesnake, crotalus atrox, via snake venomics and combinatorial peptide ligand library approaches. J Proteome Res. 2009; 8:3055-367.
• [36]Ruan Z, Liu G, Wang B, Zhou Y, Lu J, Wang Q et al.. First report of a peroxiredoxin homologue in jellyfish: molecular cloning, expression and functional characterization of CcPrx4 from Cyanea capillata. Mar Drugs. 2014; 12:214-31.
• [37]Slautterback D, Fawcett D. The development of the cnidoblasts of Hydra. J Biophys Biochem Cy. 1959; 5:441-52.
• [38]Dekhil H, Wisner A, Marrakchi N, El Ayeb M, Bon C, Karoui H. Molecular cloning and expression of a functional snake venom serine proteinase, with platelet aggregating activity, from the Cerastes cerastes viper. Biochemistry. 2003; 42:10609-18.
• [39]Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30:2114-20.
• [40]Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28:3150-2.
• [41]Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. BioMed Central Full Text
• [42]Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T et al.. The dynamic genome of Hydra. Nature. 2010; 464:592-6.
• [43]Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A et al.. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007; 317:86-94.
• [44]Lottaz C, Iseli C, Jongeneel CV, Bucher P. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics. 2003;19:103–112.
• [45]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM et al.. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-9.
• [46]Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S et al.. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011; 39:W316-22.
• [47]Bloom DA, Burnett JW, Alderslade P. Partial purification of box jellyfish (Chironex fleckeri) nematocyst venom isolated at the beachside. Toxicon. 1998; 36:1075-85.
• [48]Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970; 227:680-5.
• [49]Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004; 20:1466-7.
• [50]Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N et al.. A guided tour of the Trans-Proteomic Pipeline. Proteomics. 2010; 10:1150-9.
• [51]Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002; 74:5383-92.
• [52]Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 2003; 75:4646-58.
• [53]Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM et al.. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics. 2009; 8:2405-17.
• [54]Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F et al.. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008; 36:W465.
• [55]Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol. 2006; 55:539.
• [56]Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z et al.. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006; 34:W293-7.