期刊论文详细信息
BMC Genomics
Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics
Jessica E Garb2  Cheryl Y Hayashi1  Thomas H Clarke3  Nadia A Ayoub3  Robert A Haney2 
[1]Department of Biology, University of California, Riverside, CA 92521, USA
[2]Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA
[3]Department of Biology, Washington and Lee University, Lexington, VA 24450, USA
关键词: Spider;    Transcriptomics;    Mass spectrometry;    Venom;    Latrotoxins;    RNA-Seq;   
Others  :  1216620
DOI  :  10.1186/1471-2164-15-366
 received in 2013-12-30, accepted in 2014-05-08,  发布年份 2014
PDF
【 摘 要 】

Background

Animal venoms attract enormous interest given their potential for pharmacological discovery and understanding the evolution of natural chemistries. Next-generation transcriptomics and proteomics provide unparalleled, but underexploited, capabilities for venom characterization. We combined multi-tissue RNA-Seq with mass spectrometry and bioinformatic analyses to determine venom gland specific transcripts and venom proteins from the Western black widow spider (Latrodectus hesperus) and investigated their evolution.

Results

We estimated expression of 97,217 L. hesperus transcripts in venom glands relative to silk and cephalothorax tissues. We identified 695 venom gland specific transcripts (VSTs), many of which BLAST and GO term analyses indicate may function as toxins or their delivery agents. ~38% of VSTs had BLAST hits, including latrotoxins, inhibitor cystine knot toxins, CRISPs, hyaluronidases, chitinase, and proteases, and 59% of VSTs had predicted protein domains. Latrotoxins are venom toxins that cause massive neurotransmitter release from vertebrate or invertebrate neurons. We discovered ≥ 20 divergent latrotoxin paralogs expressed in L. hesperus venom glands, significantly increasing this biomedically important family. Mass spectrometry of L. hesperus venom identified 49 proteins from VSTs, 24 of which BLAST to toxins. Phylogenetic analyses showed venom gland specific gene family expansions and shifts in tissue expression.

Conclusions

Quantitative expression analyses comparing multiple tissues are necessary to identify venom gland specific transcripts. We present a black widow venom specific exome that uncovers a trove of diverse toxins and associated proteins, suggesting a dynamic evolutionary history. This justifies a reevaluation of the functional activities of black widow venom in light of its emerging complexity.

【 授权许可】

   
2014 Haney et al.; licensee BioMed Central Ltd.

【 预 览 】
附件列表
Files Size Format View
20150701164640344.pdf 2275KB PDF download
Figure 8. 55KB Image download
Figure 7. 36KB Image download
Figure 6. 141KB Image download
Figure 5. 56KB Image download
Figure 4. 75KB Image download
Figure 3. 77KB Image download
Figure 2. 89KB Image download
Figure 1. 60KB Image download
【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Figure 8.

【 参考文献 】
  • [1]Fry BG, Roelants K, Champagne DE, Scheib H, Tyndall JDA, King GF, Nevalainen TJ, Norman JA, Lewis RJ, Norton RS, Renjifo C, de la Vega RCR: The toxicogenomic multiverse: convergent recruitment of proteins into animal venoms. Annu Rev Genomics Hum Genet 2009, 10:483-511.
  • [2]Rash LD, Hodgson WC: Pharmacology and biochemistry of spider venoms. Toxicon 2002, 40:225-254.
  • [3]Casewell NR, Wüster W, Vonk FJ, Harrison RA, Fry BG: Complex cocktails: the evolutionary novelty of venoms. Trends Ecol Evol 2013, 28:219-229.
  • [4]Platnick NI: The World Spider Catalog, Version 14.0. [http://research.amnh.org/entomology/spiders/catalog/index.html webcite]
  • [5]King GF: The wonderful world of spiders: preface to the special Toxicon issue on spider venoms. Toxicon 2004, 43:471-475.
  • [6]Escoubas P, Sollod B, King GF: Venom landscapes: mining the complexity of spider venoms via a combined cDNA and mass spectrometric approach. Toxicon 2006, 47:650-663.
  • [7]King GF, Hardy MC: Spider-venom peptides: structure, pharmacology, and potential for control of insect pests. Annu Rev Entomol 2013, 58:475-496.
  • [8]Possani L: Peptides and genes coding for scorpion toxins that affect ion-channels. Biochimie 2000, 82:861-868.
  • [9]Olivera BM, Cruz LJ: Conotoxins, in retrospect. Toxicon 2001, 39:7-14.
  • [10]Isbister GK, White J: Clinical consequences of spider bites: recent advances in our understanding. Toxicon 2004, 43:477-492.
  • [11]Vassilevski AA, Kozlov SA, Grishin EV: Molecular diversity of spider venom. Biochemistry (Moscow) 2009, 74:1505-1534.
  • [12]Zhang Y, Chen J, Tang X, Wang F, Jiang L, Xiong X, Wang M, Rong M, Liu Z, Liang S: Transcriptome analysis of the venom glands of the Chinese wolf spider Lycosa singoriensis. Zoology 2010, 113:10-18.
  • [13]He Q, Duan Z, Yu Y, Liu Z, Liu Z, Liang S: The venom gland transcriptome of Latrodectus tredecimguttatus revealed by deep sequencing and cDNA library analysis. PLoS ONE 2013, 8:e81357.
  • [14]Kuhn-Nentwig L, Stöcklin R, Nentwig W: Venom composition and strategies in spiders. In Adv Insect Physiol. Volume 40. London: Elsevier; 2011::1-86.
  • [15]Saez NJ, Senff S, Jensen JE, Er SY, Herzig V, Rash LD, King GF: Spider-venom peptides as therapeutics. Toxins 2010, 2:2851-2871.
  • [16]Adams ME, Herold EE, Venema VJ: Two classes of channel-specific toxins from funnel web spider venom. J Comp Physiol A 1989, 164:333-342.
  • [17]Wullschleger B: Spider venom: enhancement of venom efficacy mediated by different synergistic strategies in Cupiennius salei. J Exp Biol 2005, 208:2115-2121.
  • [18]Olivera BM: E.E. Just Lecture, 1996. Conus venom peptides, receptor and ion channel targets, and drug design: 50 million years of neuropharmacology. Mol Biol Cell 1997, 8:2101-2109.
  • [19]Kiyatkin NI, Dulubova IE, Chekhovskaya IA, Grishin EV: Cloning and structure of cDNA encoding α-latrotoxin from black widow spider venom. FEBS Lett 1990, 270:127-131.
  • [20]Kiyatkin N, Dulubova I, Grishin E: Cloning and structural analysis of alpha-latroinsectotoxin cDNA. Abundance of ankyrin-like repeats. Eur J Biochem 1993, 213:121-127.
  • [21]Dulubova IE, Krasnoperov VG, Khvotchev MV, Pluzhnikov KA, Volkova TM, Grishin EV, Vais H, Bell DR, Usherwood PN: Cloning and structure of delta-latroinsectotoxin, a novel insect-specific member of the latrotoxin family: functional expression requires C-terminal truncation. J Biol Chem 1996, 271:7535-7543.
  • [22]Danilevich VN, Luk’ianov SA, Grishin EV: Cloning and structure of gene encoded alpha-latrocrustotoxin from the black widow spider venom. Bioorg Khim 1999, 25:537-547.
  • [23]Ushkaryov Y: α-Latrotoxin: from structure to some functions. Toxicon 2002, 40:1-5.
  • [24]Rohou A, Nield J, Ushkaryov YA: Insecticidal toxins from black widow spider venom. Toxicon 2007, 49:531-549.
  • [25]Graudins A, Little MJ, Pineda SS, Hains PG, King GF, Broady KW, Nicholson GM: Cloning and activity of a novel α-latrotoxin from red-back spider venom. Biochem Pharmacol 2012, 83:170-183.
  • [26]Garb JE, Hayashi CY: Molecular evolution of alpha-Latrotoxin, the exceptionally potent vertebrate neurotoxin in black widow spider venom. Mol Biol Evol 2013, 30:999-1014.
  • [27]Ushkaryov YA, Volynski KE, Ashton AC: The multiple actions of black widow spider toxins and their selective use in neurosecretion studies. Toxicon 2004, 43:527-542.
  • [28]Pescatori M, Bradbury A, Bouet F, Gargano N, Mastrogiacomo A, Grasso A: The cloning of a cDNA encoding a protein (latrodectin) which co-purifies with the alpha-latrotoxin from the black widow spider Latrodectus tredecimguttatus (Theridiidae). Eur J Biochem 1995, 230:322-328.
  • [29]Volkova TM, Pluzhnikov KA, Woll PG, Grishin EV: Low molecular weight components from black widow spider venom. Toxicon 1995, 33:483-489.
  • [30]Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y: RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517.
  • [31]Yuan C, Jin Q, Tang X, Hu W, Cao R, Yang S, Xiong J, Xie C, Xie J, Liang S: Proteomic and peptidomic characterization of the venom from the Chinese bird spider, Ornithoctonus huwena Wang. J Proteome Res 2007, 6:2792-2801.
  • [32]Tang X, Zhang Y, Hu W, Xu D, Tao H, Yang X, Li Y, Jiang L, Liang S: Molecular diversification of peptide toxins from the tarantula Haplopelma hainanum (Ornithoctonus hainana) venom based on transcriptomic, peptidomic, and genomic analyses. J Proteome Res 2010, 9:2550-2564.
  • [33]Maretić Z: Latrodectism: variations in clinical manifestations provoked by Latrodectus species of spiders. Toxicon 1983, 21:457-466.
  • [34]Isbister GK, Gray MR: Latrodectism: a prospective cohort study of bites by formally identified redback spiders. Med J Aust 2003, 179:88-91.
  • [35]Silva J-P, Suckling J, Ushkaryov Y: Penelope’s web: using α-latrotoxin to untangle the mysteries of exocytosis. J Neurochem 2009, 111:275-290.
  • [36]Huang X: CAP3: a DNA sequence assembly program. Genome Res 1999, 9:868-877.
  • [37]Clarke TH, Garb JE, Hayashi CY, Haney RA, Lancaster AK, Corbett S, Ayoub NA: Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit. BMC Genomics 2014, 15:365.
  • [38]Grishin EV: Black widow spider toxins: the present and the future. Toxicon 1998, 36:1693-1701.
  • [39]Li J, Mahajan A, Tsai M-D: Ankyrin repeat: a unique motif mediating protein-protein interactions. Biochemistry (Mosc) 2006, 45:15168-15178.
  • [40]Von Reumont BM, Blanke A, Richter S, Alvarez F, Bleidorn C, Jenner RA: The first venomous crustacean revealed by transcriptomics and functional morphology: remipede venom glands express a unique toxin cocktail dominated by enzymes and a neurotoxin. Mol Biol Evol 2014, 31:48-58.
  • [41]Jungo F, Bairoch A: Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase. Toxicon 2005, 45:293-301.
  • [42]Coddington JA: Phylogeny and classification of spiders. In Spiders N Am Identif Man. American Arachnological Society; 2005:18-24.
  • [43]Vassilevski AA, Fedorova IM, Maleeva EE, Korolkova YV, Efimova SS, Samsonova OV, Schagina LV, Feofanov AV, Magazanik LG, Grishin EV: Novel class of spider toxin: active principle from the yellow sac spider Cheiracanthium punctorium venom is a unique two-domain polypeptide. J Biol Chem 2010, 285:32293-32302.
  • [44]Kuhn-Nentwig L, Fedorova IM, Lüscher BP, Kopp LS, Trachsel C, Schaller J, Vu XL, Seebeck T, Streitberger K, Nentwig W, Sigel E, Magazanik LG: A venom-derived neurotoxin, CsTx-1, from the spider Cupiennius salei exhibits cytolytic activities. J Biol Chem 2012, 287:25640-25649.
  • [45]Sollod BL, Wilson D, Zhaxybayeva O, Gogarten JP, Drinkwater R, King GF: Were arachnids the first to use combinatorial peptide libraries? Peptides 2005, 26:131-139.
  • [46]Südhof TC: alpha-Latrotoxin and its receptors: neurexins and CIRL/latrophilins. Annu Rev Neurosci 2001, 24:933-962.
  • [47]Rowen L, Young J, Birditt B, Kaur A, Madan A, Philipps DL, Qin S, Minx P, Wilson RK, Hood L, Graveley BR: Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics 2002, 79:587-597.
  • [48]Reissner C, Runkel F, Missler M: Neurexins. Genome Biol 2013, 14:213. BioMed Central Full Text
  • [49]Finkelstein A, Rubin LL, Tzeng MC: Black widow spider venom: effect of purified toxin on lipid bilayer membranes. Science 1976, 193:1009-1011.
  • [50]Mironov SL, Sokolov YV, Chanturiya AN, Lishko VK: Channels produced by spider venoms in bilayer lipid membrane: mechanisms of ion transport and toxic action. Biochim Biophys Acta 1986, 862:185-198.
  • [51]Wagh DA, Rasse TM, Asan E, Hofbauer A, Schwenkert I, Dürrbeck H, Buchner S, Dabauvalle M-C, Schmidt M, Qin G: Bruchpilot, a protein with homology to ELKS/CAST, is required for structural integrity and function of synaptic active zones in Drosophila. Neuron 2006, 49:833-844.
  • [52]Zipursky SL, Wojtowicz WM, Hattori D: Got diversity? Wiring the fly brain with Dscam. Trends Biochem Sci 2006, 31:581-588.
  • [53]Hortsch M, Nagaraj K, Godenschwege TA: The interaction between L1-type proteins and ankyrins - a master switch for L1-type CAM function. Cell Mol Biol Lett 2008, 14:57-69.
  • [54]Laurén J, Airaksinen MS, Saarma M, Timmusk T: A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. Genomics 2003, 81:411-421.
  • [55]Grueber WB, Yang C-H, Ye B, Jan Y-N: The development of neuronal morphology in insects. Curr Biol 2005, 15:R730-R738.
  • [56]Duda TF, Palumbi SR: Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc Natl Acad Sci 1999, 96:6820-6823.
  • [57]Chen J, Zhao L, Jiang L, Meng E, Zhang Y, Xiong X, Liang S: Transcriptome analysis revealed novel possible venom components and cellular processes of the tarantula Chilobrachys jingzhao venom gland. Toxicon 2008, 52:794-806.
  • [58]Sedgwick SG, Smerdon SJ: The ankyrin repeat: a diversity of interactions on a common structural framework. Trends Biochem Sci 1999, 24:311-316.
  • [59]Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L: Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct 2012, 7:18. BioMed Central Full Text
  • [60]Perret BA: Proteolytic activity of tarantula venoms due to contamination with saliva. Toxicon Off J Int Soc Toxinology 1977, 15:505-510.
  • [61]Matsui T, Fujimura Y, Titani K: Snake venom proteases affecting hemostasis and thrombosis. Biochim Biophys Acta 2000, 1477:146-156.
  • [62]Smith D, Russell F: Structure of the venom gland of the black widow spider Latrodectus mactans. A preliminary light and electron microscopic study. In Anim Toxins. Edited by Russell F, Saunders P. Oxford: Pergamon; 1966:1-15.
  • [63]Vetter RS, Isbister GK: Medical aspects of spider bites. Annu Rev Entomol 2008, 53:409-429.
  • [64]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29:644-652.
  • [65]Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 2013, 8:1494-1512.
  • [66]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
  • [67]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
  • [68]Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. BioMed Central Full Text
  • [69]Finn RD, Clements J, Eddy SR: HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011, 39(suppl):W29-W37.
  • [70]Young MD, Wakefield MJ, Smyth GK, Oshlack A: Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 2010, 11:R14. BioMed Central Full Text
  • [71]Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R: InterProScan: protein domains identifier. Nucleic Acids Res 2005, 33(Web Server):W116-W120.
  • [72]Naamati G, Askenazi M, Linial M: ClanTox: a classifier of short animal toxins. Nucleic Acids Res 2009, 37(Web Server):W363-W368.
  • [73]Kaplan N, Morpurgo N, Linial M: Novel families of toxin-like peptides in insects and mammals: a computational approach. J Mol Biol 2007, 369:553-566.
  • [74]Gracy J, Le-Nguyen D, Gelly J-C, Kaas Q, Heitz A, Chiche L: KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. Nucleic Acids Res 2007, 36(Database):D314-D319.
  • [75]Emanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007, 2:953-971.
  • [76]Wolters DA, Washburn MP, Yates JR: An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001, 73:5683-5690.
  • [77]Eng JK, McCormack AL, Yates JR: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5:976-989.
  • [78]Papadopoulos JS, Agarwala R: COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 2007, 23:1073-1079.
  • [79]Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009, 25:1972-1973.
  • [80]Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP: MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012, 61:539-542.
  • [81]Stamatakis A: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30:1312-1313.
  • [82]McCowan C, Garb JE: Recruitment and diversification of an ecdysozoan family of neuropeptide hormones for black widow spider venom expression. Gene 2014, 536:366-375.
  文献评价指标  
  下载次数:88次 浏览次数:19次