Journal of Molecular Evolution

, Volume 86, Issue 1, pp 58–67 | Cite as

Ancient Diversification of Three-Finger Toxins in Micrurus Coral Snakes

  • Daniel Dashevsky
  • Bryan G. Fry
Original Article


Coral snakes, most notably the genus Micrurus, are the only terrestrial elapid snakes in the Americas. Elapid venoms are generally known for their potent neurotoxicity which is usually caused by Three-Finger Toxin (3FTx) proteins. These toxins can have a wide array of functions that have been characterized from the venom of other elapids. We examined publicly available sequences from Micrurus 3FTx to show that they belong to 8 monophyletic clades that diverged as deep in the 3FTx phylogenetic tree as the other clades with characterized functions. Functional residues from previously characterized clades of 3FTx are not well conserved in most of the Micrurus toxin clades. We also analyzed the patterns of selection on these toxins and find that they have been diversifying at different rates, with some having undergone extreme diversifying selection. This suggests that Micrurus 3FTx may contain a previously underappreciated functional diversity that has implications for the clinical outcomes of bite victims, the evolution and ecology of the genus, as well as the potential for biodiscovery efforts focusing on these toxins.


Coral snake Elapid Micrurus Venom Three-finger toxin 3FTx 



D.D. is supported by the International Postgraduate Research Scholarship from The University of Queensland.

Supplementary material (22 kb)
Supplementary material 1 (NEXUS 22 KB)
239_2017_9825_MOESM2_ESM.nwk (10 kb)
Supplementary material 2 (NWK 10 KB) (11 kb)
Supplementary material 3 (NEXUS 10 KB) (5 kb)
Supplementary material 4 (NEXUS 5 KB) (2 kb)
Supplementary material 5 (NEXUS 1 KB) (3 kb)
Supplementary material 6 (NEXUS 2 KB) (1 kb)
Supplementary material 7 (NEXUS 1 KB) (1 kb)
Supplementary material 8 (NEXUS 1 KB) (8 kb)
Supplementary material 9 (NEXUS 8 KB)
239_2017_9825_MOESM10_ESM.r (2 kb)
Supplementary material 10 (R 1 KB)


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410CrossRefPubMedGoogle Scholar
  2. Antil S, Servent D, Ménez A (1999) Variability among the sites by which curaremimetic toxins bind to torpedo acetylcholine receptor, as revealed by identification of the functional residues of α-cobratoxin. J Biol Chem 274 (49): 34,851–34,858Google Scholar
  3. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2013) GenBank. Nucleic Acids Res 41(Database issue):D36–D42PubMedGoogle Scholar
  4. Bucaretchi F, Capitani EMD, Vieira RJ, Rodrigues CK, Zannin M Jr, Casais-e Silva NJDS., Hyslop LL S (2016) Coral snake bites (Micrurus spp.) in Brazil: a review of literature reports. Clin Toxicol 54(3):222–234CrossRefGoogle Scholar
  5. Cañas CA, Castro-Herrera F, Castaño Valencia S (2017) Envenomation by the red-tailed coral snake (Micrurus mipartitus) in Colombia. J Venom Anim Toxins Trop Dis 23(1):9CrossRefGoogle Scholar
  6. Carbajal-Saucedo A, López-Vera E, Bénard-Valle M, Smith EN, Zamudio F, de Roodt AR, Olvera-Rodríguez A (2013) Isolation, characterization, cloning and expression of an alpha-neurotoxin from the venom of the Mexican coral snake Micrurus laticollaris (Squamata: Elapidae). Toxicon 66:64–74CrossRefPubMedGoogle Scholar
  7. Chang CC (1999) Looking back on the discovery of α-bungarotoxin. J Biomed Sci 6(6):368–375PubMedGoogle Scholar
  8. Ciscotto PH, Rates B, Silva DA, Richardson M, Silva LP, Andrade H, Donato MF, Cotta GA, Maria WS, Rodrigues RJ (2011) Venomic analysis and evaluation of antivenom cross-reactivity of South American Micrurus species. J Proteom 74(9):1810–1825CrossRefGoogle Scholar
  9. Consortium TU (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45(D1):D158–D169CrossRefGoogle Scholar
  10. da Silva NJ, Aird SD (2001) Prey specificity, comparative lethality and compositional differences of coral snake venoms. Comp Biochem Physiol C 128(3):425–456CrossRefGoogle Scholar
  11. Diochot S, Baron A, Salinas M, Douguet D, Scarzello S, Dabert-Gay AS, Debayle D, Friend V, Alloui A, Lazdunski M, Lingueglia E (2012) Black mamba venom peptides target acid-sensing ion channels to abolish pain. Nature 490(7421):552–555CrossRefPubMedGoogle Scholar
  12. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797CrossRefPubMedPubMedCentralGoogle Scholar
  13. Fry BG, Wster W, Kini RM, Brusic V, Khan A, Venkataraman D, Rooney AP (2003) Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J Mol Evol 57(1):110–129CrossRefPubMedGoogle Scholar
  14. Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150–3152CrossRefPubMedPubMedCentralGoogle Scholar
  15. Gong N, Armugam A, Jeyaseelan K (1999) Postsynaptic short-chain neurotoxins from Pseudonaja textilis. FEBS J 265(3):982–989Google Scholar
  16. Harvey AL (2014) Toxins and drug discovery. Toxicon 92:193–200CrossRefPubMedGoogle Scholar
  17. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858CrossRefPubMedPubMedCentralGoogle Scholar
  18. Kelly CMR, Barker NP, Villet MH, Broadley DG (2009) Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene. Cladistics 25(1):38–63CrossRefGoogle Scholar
  19. King GF (2013) Venoms to drugs: translating venom peptides into therapeutics. Aust Biochem 44(3):13–15Google Scholar
  20. King G (2015) Venoms to drugs: venom as a source for the development of human therapeutics. Royal Society of ChemistryGoogle Scholar
  21. Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30(22):3276–3278CrossRefPubMedPubMedCentralGoogle Scholar
  22. Lee MSY, Sanders KL, King B, Palci A (2016) Diversification rates and phenotypic evolution in venomous snakes (Elapidae). Open Sci 3(1):150,277Google Scholar
  23. Leite dos Santos GG, Casais e Silva LL, Pereira Soares MB, Villarreal CF (2012) Antinociceptive properties of Micrurus lemniscatus venom. Toxicon 60(6):1005–1012CrossRefPubMedGoogle Scholar
  24. Li W, Godzik A (2006) CD–HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658–1659CrossRefPubMedGoogle Scholar
  25. Lomonte B, Rey-Suárez P, Fernández J, Sasa M, Pla D, Vargas N, Bénard-Valle M, Sanz L, Corrêa-Netto C, Núñez V, Alape-Girón A, Alagón A, Gutiérrez JM, Calvete JJ (2016) Venoms of Micrurus coral snakes: evolutionary trends in compositional patterns emerging from proteomic analyses. Toxicon 122:7–25CrossRefPubMedGoogle Scholar
  26. Manock SR, Suarez G, Graham D, Avila-Aguero ML, Warrell DA (2008) Neurotoxic envenoming by South American coral snake (Micrurus lemniscatus helleri): case report from eastern Ecuador and review. Trans R Soc Trop Med Hyg 102(11):1127–1132CrossRefPubMedGoogle Scholar
  27. Margres MJ, Aronow K, Loyacano J, Rokyta DR (2013) The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms. BMC Genom 14(1):1CrossRefGoogle Scholar
  28. Moreira K, Prates M, Andrade F, Silva L, Beiro P, Kushmerick C, Naves L, Bloch C (2010) Frontoxins, three-finger toxins from Micrurus frontalis venom, decrease miniature endplate potential amplitude at frog neuromuscular junction. Toxicon 56(1):55–63CrossRefPubMedGoogle Scholar
  29. Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Pond SLK (2012) Detecting individual sites subject to episodic diversifying selection. PLOS Genet 8 (7): e1002,764Google Scholar
  30. Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Pond K, Scheffler LS K (2013) FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol 30(5):1196–1205CrossRefPubMedPubMedCentralGoogle Scholar
  31. Nelsen DR, Nisani Z, Cooper AM, Fox GA, Gren ECK, Corbit AG, Hayes WK (2014) Poisons, toxungens, and venoms: redefining and classifying toxic biological secretions and the organisms that employ them. Biol Rev 89(2):450–465CrossRefPubMedGoogle Scholar
  32. Norris RL, Pfalzgraf RR, Laing G (2009) Death following coral snake bite in the United States first documented case (with ELISA confirmation of envenomation) in over 40 years. Toxicon 53(6):693–697CrossRefPubMedGoogle Scholar
  33. Olamendi-Portugal T, Batista CVF, Restano-Cassulini R, Pando V, Villa-Hernandez O, Zavaleta-Martínez-Vargas A, Salas-Arruz MC, de la Vega RCR, Becerril B, Possani LD (2008) Proteomic analysis of the venom from the fish eating coral snake Micrurus surinamensis: Novel toxins, their function and phylogeny. Proteomics 8(9):1919–1932CrossRefPubMedGoogle Scholar
  34. Otero-Patiño DR (2014) Snake bites in Colombia. In: Gopalakrishnakone P, Faiz SMA, Gnanathasan CA, Habib AG, Fernando R, Yang CC (eds) Clinical toxinology. Springer, Netherlands, pp 1–42Google Scholar
  35. Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17(8):700–712CrossRefPubMedGoogle Scholar
  36. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimeraa visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612CrossRefPubMedGoogle Scholar
  37. Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5):676–679CrossRefPubMedGoogle Scholar
  38. Pu XC, Wong PTH, Gopalakrishnakone P (1995) A novel analgesic toxin (hannalgesin) from the venom of king cobra (Ophiophagus hannah). Toxicon 33(11):1425–1431CrossRefPubMedGoogle Scholar
  39. Pyron RA, Burbrink FT, Wiens JJ (2013) A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol 13:93CrossRefPubMedPubMedCentralGoogle Scholar
  40. Rey-Suárez P, Núñez V, Gutiérrez JM, Lomonte B (2011) Proteomic and biological characterization of the venom of the redtail coral snake, Micrurus mipartitus (Elapidae), from Colombia and Costa Rica. J Proteom 75(2):655–667CrossRefGoogle Scholar
  41. Rey-Suárez P, Floriano RS, Rostelato-Ferreira S, Saldarriaga-Córdoba M, Núñez V, Rodrigues-Simioni L, Lomonte B (2012) Mipartoxin-I, a novel three-finger toxin, is the major neurotoxic component in the venom of the redtail coral snake Micrurus mipartitus (Elapidae). Toxicon 60(5):851–863CrossRefPubMedGoogle Scholar
  42. Rey-Suárez P, Núñez V, Fernández J, Lomonte B (2016) Integrative characterization of the venom of the coral snake Micrurus dumerilii (Elapidae) from Colombia: Proteome, toxicity, and cross-neutralization by antivenom. J Proteom 136:262–273CrossRefGoogle Scholar
  43. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539–542CrossRefPubMedPubMedCentralGoogle Scholar
  44. Rosenfeld G (1971) Symptomatology, pathology and treatment of snake bites in South America. Venomous animals and their venoms, vol 2. Academic Press, pp 345–384Google Scholar
  45. Rosso JP, Schwarz JR, Diaz-Bustamante M, Céard B, Gutiérrez JM, Kneussel M, Pongs O, Bosmans F, Bougis PE (2015). MmTX1 and MmTX2 from coral snake venom potently modulate GABAA receptor activity. Proc Natl Acad Sci 112:E891–E900CrossRefPubMedPubMedCentralGoogle Scholar
  46. Roze JA (1996) Coral snakes of the Americas: biology, identification, and venoms. Krieger Publishing Company, MalabarGoogle Scholar
  47. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504CrossRefPubMedPubMedCentralGoogle Scholar
  48. Sunagar K, Jackson T, Undheim E, Ali S, Antunes A, Fry B (2013) Three-fingered RAVERs: rapid accumulation of variations in exposed residues of snake venom toxins. Toxins 5(11):2172–2208CrossRefPubMedPubMedCentralGoogle Scholar
  49. Terra AL, Moreira-Dill LS, Simes-Silva R, Monteiro JRN, Cavalcante WL, Gallacci M, Barros NB, Nicolete R, Teles CB, Medeiros PS, Zanchi FB, Zuliani JP, Calderon LA, Stábeli RG, Soares AM (2015) Biological characterization of the Amazon coral Micrurus spixii snake venom: Isolation of a new neurotoxic phospholipase A2. Toxicon 103:1–11CrossRefPubMedGoogle Scholar
  50. Uetz P, Freed P, Hoek J (2016) The Reptile Database.
  51. Utkin Y, Sunagar K, Jackson T, Reeks T, Fry B (2015) Three-finger toxins (3FTxs). In: Fry BG (ed) Venomous reptiles and their toxins: evolution, pathophysiology and biodiscovery. Oxford University Press, Oxford 215–227Google Scholar
  52. Wallach V, Williams KL, Boundy J (2014) Snakes of the world: a catalogue of living and extinct species. CRC Press, Baco RatonCrossRefGoogle Scholar
  53. Wyckoff GJ, Wang W, Wu CI (2000) Rapid evolution of male reproductive genes in the descent of man. Nature 403(6767):304–309CrossRefPubMedGoogle Scholar
  54. Yang DC, Deuis JR, Dashevsky D, Dobson J, Jackson TNW, Brust A, Xie B, Koludarov I, Debono J, Hendrikx I, Hodgson WC, Josh P, Nouwens A, Baillie GJ, Bruxner TJC, Alewood PF, Lim KKP, Frank N, Vetter I, Fry BG (2016) The Snake with the scorpions sting: novel three-finger toxin sodium channel activators from the venom of the long-glanded blue coral snake (Calliophis bivirgatus). Toxins 8(10):303CrossRefPubMedCentralGoogle Scholar
  55. Yang DC, Dobson J, Cochran C, Dashevsky D, Arbuckle K, Benard M, Boyer L, Alagn A, Hendrikx I, Hodgson WC, Fry BG (2017) The bold and the beautiful: a neurotoxicity comparison of New World coral snakes in the Micruroides and Micrurus genera and relative neutralization by antivenom. Neurotox Res 32(3):487–495CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Venom Evolution Lab, School of Biological SciencesUniversity of QueenslandSt LuciaAustralia

Personalised recommendations