Molecular evolution of the infrared sensory gene TRPA1 in snakes and implications for functional studies

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Geng, Jie ^a   Liang, Dan ^a   Jiang, Ke ^a,b   Zhang, Peng ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; TRANSIENT RECEPTOR POTENTIAL CHANNEL A1; CALCIUM; CALCIUM CHANNEL; ION; PRIMER DNA;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; FUNCTIONAL ASSESSMENT; GENE; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC VARIABILITY; INFRARED RADIATION; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; NONHUMAN; NUCLEOTIDE SEQUENCE; SNAKE; SPECIES DIFFERENCE; TRPA1 GENE; TRPV1 GENE; VERTEBRATE; ANIMAL; CHEMISTRY; DNA SEQUENCE; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PRESSURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; CALCIUM; CALCIUM CHANNELS; DNA PRIMERS; EVOLUTION, MOLECULAR; INFRARED RAYS; IONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PRESSURE; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SNAKES; SPECIES SPECIFICITY;

EID: 82855168080     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028644     Document Type: Article

References (36)

1. Grace MS, Woodward OM, Church DR, Calisch G, (2001) Prey targeting by the infrare-imaging snake Python: effects of experimental and congenital visual deprivation. Behav Brain Res 119: 23-31.
2. Goris RC, (2011) Infrared Organs of Snakes: An Integral Part of Vision. Journal of Herpetology 45 (1): 2-14.
3. Bullock TH, Diecke PJ, (1956) Properties of an infra-red receptor. J Physiol 134: 47-87.
4. Krochmal AR, Bakken GS, LaDuc TJ, (2004) Heat in evolution's kitchen: evolutionary perspectives on the functions and origin of the facial pit of pitvipers (Viperidae: Crotalinae). J Exp Biol 207: 4231-4238.
5. Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, et al. (2010) Molecular basis of infrared detection by snakes. Nature 464: 1006-1011.
6. Ebert J, (2007) Infrared Sense in Snakes - Behavioural and Anatomical Examinations (Crotalus atrox, Python regius, Corallus hortulanus). Dr rer. nat. thesis, Rheinische Friedrich Wilhelms Univ. Bonn., Germany.
7. Briscoe AD, Bybee SM, Bernard GD, Yuan F, Sison-Mangus MP, et al. (2010) Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies. Proc Natl Acad Sci U S A 107: 3628-3633.
8. Li G, Wang JH, Rossiter SJ, Jones G, Cotton JA, et al. (2008) The hearing gene Prestin reunites echolocating bats. Proc Natl Acad Sci USA 105: 13959-13964.
9. Shi P, Zhang J, Yang H, Zhang YP, (2003) Adaptive diversification of bitter taste receptor genes in Mammalian evolution. Mol Biol Evol 20: 805-814.
10. Yokoyama S, Tada T, Zhang H, Britt L, (2008) Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A 105: 13480-13485.
11. Yokoyama S, Altun A, DeNardo DF, (2011) Molecular convergence of infrared vision in snakes. Mol Biol Evol 28 (1): 45-48.
12. Corey DP, García-Añoveros J, Holt JR, Kwan KY, Lin SY, et al. (2004) TRPA1 is a candidate for the mechanosensitive transduction channel of vertebrate hair cells. Nature 432: 723-730.
13. Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JW Jr, et al. (2008) Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear Loci in snakes. Syst Biol 57 (3): 420-431.
14. Vidal N, Rage JC, Couloux A, Hedges SB, (2009) Snakes. (Serpentes). In: Hedeges SB, Kumar S, editors. The timetree of life New York Oxford University Press pp. 390-397.
15. Saito S, Fukuta N, Shingai R, Tominaga M, (2011) Evolution of Vertebrate Transient Receptor Potential Vanilloid 3 Channels: Opposite Temperature Sensitivity between Mammals and Western Clawed Frogs. PLoS Genet 7 (4): e1002041.
16. Neeper MP, Liu Y, Hutchinson TL, Wang Y, Flores CM, et al. (2007) Activation properties of heterologously expressed mammalian TRPV2: evidence for species dependence. J Biol Chem 282: 15894-15902.
17. Brauchi S, Orta G, Salazar M, Rosenmann E, Latorre R, (2006) A hot-sensing cold receptor: C-terminal domain determines thermosensation in transient receptor potential channels. J Neurosci 26: 4835-4840.
18. Vlachova V, Teisinger J, Susankova K, Lyfenko A, Ettrich R, et al. (2003) Functional role of C-terminal cytoplasmic tail of rat vanilloid receptor 1. J Neurosci 23: 1340-1350.
19. Li Y, Liu Z, Shi P, Zhang J, (2010) The hearing gene Prestin unites echolocating bats and whales. Curr Biol 20: R55-R56.
20. Kornegay JR, Schilling JW, Wilson AC, (1994) Molecular adaptation of a leaf-eating bird: Stomach lysozyme of the hoatzin. Mol Biol Evol 11: 921-928.
21. Zhang JZ, (2006) Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nat Genet 38: 819-823.
22. Christin PA, Salamin N, Savolainen V, Duvall MR, Besnard G, (2007) C4 photosynthesis evolved in grasses via parallel adaptive genetic changes. Curr Biol 17: 1241-1247.
23. Stewart CB, Schilling JW, Wilson AC, (1987) Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330: 401-404.
24. Gaudet R, (2008) A primer on ankyrin repeat function in TRP channels and beyond. Mol Biosyst 4: 372-379.
25. Phelps CB, Wang RR, Choo SS, Gaudet R, (2009) Differential regulation of TRPV1, TRPV3, and TRPV4 sensitivity through a conserved binding site on the ankyrin repeat domain. J Biol Chem 285: 731-40.
26. Sotomayor M, Corey DP, Schulten K, (2005) In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats. Structure 13: 669-682. 37. Lee G, Abdi K, Jiang Y, Michaely P, Bennett V,et al. (2006) Nanospring behaviour of ankyrin repeats. Nature 440: 246-249.
27. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
28. Hall A, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
29. Nylander JAA, (2004) MrModeltest v2.Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Sweden.
30. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of Taxa and mixed models. Bioinformatics 22 (21): 2688-2690.
31. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
32. Pride DT, (2000) SWAAP-a tool for analyzing substitutions and similarity in multiple alignments.
33. Nei M, Gojobori T, (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
34. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
35. Kosakovsky Pond SL, Frost SD, (2005) A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol 22: 478-485.
36. Kosakovsky Pond SL, Frost SDW, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.