Unique structural characteristics and evolution of a cluster of venom phospholipase A2 isozyme genes of Protobothrops flavoviridis snake

Gene

Volumn 461, Issue 1-2, 2010, Pages 15-25

  Ikeda, Naoki ^a   Chijiwa, Takahito ^a   Matsubara, Kazumi ^b   Oda Ueda, Naoko ^a   Hattori, Shosaku ^c   Matsuda, Yoichi ^b   Ohno, Motonori ^a  

^a SOJO UNIVERSITY   (Japan)

^b HOKKAIDO UNIVERSITY   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

CR1 LINE; Multiplication; Phospholipase A2 gene; Protobothrops flavoviridis; Retrotransposition; Unequal crossing over

Indexed keywords

PHOSPHOLIPASE A2; RNA DIRECTED DNA POLYMERASE; SNAKE VENOM;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMINO ACID SEQUENCE; ARTICLE; GENE; GENE DUPLICATION; GENE INACTIVATION; GENE STRUCTURE; GENETIC CODE; GENETIC LINKAGE; LIVER; LONG INTERSPERSED REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTOBOTHROPS FLAVOVIRIDIS; RETROPOSON; SEQUENCE ANALYSIS; SNAKE;

AMINO ACID SEQUENCE; ANIMALS; BASE PAIRING; BASE SEQUENCE; CHICKENS; CROTALID VENOMS; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; GENOME; IN SITU HYBRIDIZATION, FLUORESCENCE; ISOENZYMES; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTAGENESIS, INSERTIONAL; PHOSPHOLIPASES A2; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; REGULATORY SEQUENCES, NUCLEIC ACID; RNA-DIRECTED DNA POLYMERASE; SEQUENCE DELETION; VIPERIDAE;

CROTALINAE; SERPENTES; TRIMERESURUS FLAVOVIRIDIS; VIPERINAE;

EID: 77954815698     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2010.04.001     Document Type: Article

References (63)

1. Agarwal M., Bensaadi N., Salvado J.C., Campbell K., Mouchés C. Characterization and genetic organization of full-length copies of a LINE retrotransposon family dispersed in the genome of Culex pipiens mosquitoes. Insect Biochem. Mol. Biol. 1993, 23:621-629.
2. Besansky N.J. A retrotransposable element from the mosquito Anopheles gambiae. Mol. Cell. Biol. 1990, 10:863-871.
3. Blin N., Stafford D.W. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 1976, 3:2303-2308.
4. Cambareri E.B., Helber J., Kinsey J.A. Tad-1, an active LINE-like element of Neurospora crassa. Mol. Gen. Genet. 1994, 242:658-665.
5. 2 in pit viper venoms. Biochem. J. 2004, 381:25-34.
6. 2 isoenzymes of Trimeresurus flavoviridis snakes in the southwestern islands of Japan. Biochem. J. 2000, 347:491-499.
7. 2 isozymes. J. Mol. Evol. 2003, 56:286-293.
8. 2. J. Mol. Evol. 2003, 57:546-554.
9. 2. Toxicon 2005, 46:185-195.
10. Ching A.T.C., et al. Some aspects of the venom proteome of the Colubridae snake Philodryas olfersii revealed from a Duvernoy's (venom) gland transcriptome. FEBS Lett. 2006, 580:4417-4422.
11. Cost G.J., Feng Q., Jacquier A., Boeke J.D. Human L1 element target-primed reverse transcription in vivo. EMBO J. 2002, 21:5899-5910.
12. 2 at 1.7Å resolution. J. Mol. Biol. 1981, 147:97-123.
13. 2 according to sequence. Evolutionary and pharmacological implications. Eur. J. Biochem. 1983, 137:545-551.
14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
15. Freeman S., Herron J.C. Evolutionary Analysis 2001, Prentice Hall, Upper Saddle river, NJ. 2nd ed.
16. Haas N.B., Grabowski J.M., Sivitz A.B., Burch J.B. Chicken repeat 1 (CR1) elements, which define an ancient family of vertebrate non-LTR retrotransposons, contain two closely spaced open reading frames. Gene 1997, 197:305-309.
17. He C., Nourse J.P., Kelemu S., Irwin J.A., Manners J.M. CgT1: a non-LTR retrotransposon with restricted distribution in the fungal phytopathogen Colletotrichum gloeosporioides. Mol. Gen. Genet. 1996, 252:320-331.
18. 2 from the venom of the cottonmouth snake at 2.0-Å resolution. J. Biol. Chem. 1990, 265:17649-17656.
19. Ichiyanagi K., Okada N. Mobility pathways for vertebrates L1, L2, CR1, and RTE clade retrotransposons. Mol. Biol. Evol. 2008, 25:1148-1157.
20. 2 diversity and polymorphism in European viper venoms: paradoxical molecular evolution in Viperinae. Toxicon 2007, 50:1140-1161.
21. John J.S., Quinn T.W. Identification of novel CR1 subfamilies in an avian order with recently active elements. Mol. Phyl. Evol. 2008, 49:1008-1014.
22. John T.R., Smith L.A., Kaiser I.I. Genomic sequences encoding the acidic and basic subunits of Mojave toxin: unusually high sequence identity of non-coding regions. Gene 1994, 139:229-239.
23. Kajikawa M., Ohshima K., Okada N. Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol. Biol. Evol. 1997, 14:1206-1217.
24. Kajikawa M., Ichiyanagi K., Tanaka N., Okada N. Isolation and characterization of active LINE and SINEs from eel. Mol. Biol. Evol. 2005, 22:673-682.
25. 2. Biochimie 2004, 86:211-219.
26. 2. Biochem. Int. 1992, 28:895-903.
27. Kimura M. The rate of molecular evolution considered from the standpoint of population genetics. Proc. Natl. Acad. Sci. USA 1969, 63:1181-1188.
28. 2 with low activity, from Trimeresurus flavoviridis venom. J. Biochem. (Tokyo) 1990, 107:400-408.
29. Liu Q., et al. A catalog for transcripts in the venom gland of the Agkistrodon acutus: identification of the toxins potentially involved in coagulopathy. Biochem. Biophys. Res. Commun. 2006, 341:522-531.
30. 2 from the venom of Trimeresurus jerdonii snake. Toxicon 2002, 40:1313-1319.
31. Luan D.D., Korman M.H., Jakubczak J.L., Eickbush T.H. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 1993, 72:595-605.
32. Malik H.S., Burke W.D., Eickbush T.H. The age and evolution of non-LTR retrotransposable elements. Mol. Biol. Evol. 1999, 16:793-805.
33. 2 with lysine in place of aspartate 49. Functional consequences for calcium and substrate binding. J. Biol. Chem. 1984, 259:13839-13843.
34. Matsuda Y., Chapman V.M. Application of fluorescence in situ hybridization in genome analysis of the mouse. Electrophoresis 1995, 16:261-272.
35. Meyers S., Bottolo L., Freeman C., McVean G., Donnell P. A fine-scale map of recombination rates and hotspots across Human genome. Science 2005, 310:321-324.
36. 2 isozymes. Proc. Natl. Acad. Sci. USA 1993, 90:5964-5968.
37. 2 isozyme genes. Proc. Natl. Acad. Sci. USA 1995, 92:5605-5609.
38. Nei M., Rooney A.P. Concerted and birth-and-death evolution of multigene families. Annu. Rev. Genet. 2005, 39:121-152.
39. 2, and consequent revision of the amino acid sequence. J. Biochem. (Tokyo) 1990, 108:816-821.
40. 2 isozymes. Proc. Natl. Acad. Sci. USA 1992, 89:8557-8561.
41. Ogiwara I., Miya M., Ohshima K., Okada N. V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrated genomes and retain a strongly conserved segment within each repetitive unit. Genome Res. 2002, 12:316-324.
42. Ohno M., et al. Molecular evolution of snake toxins: is the functional diversity of snake toxins associated with a mechanism of accelerated evolution?. Progress in Nucleic Acid Research and Molecular Biology 1998, vol 59:307-364. Academic Press, NY. K. Moldave (Ed.).
43. Ohno M., Ogawa T., Oda-Ueda N., Chijiwa T., Hattori S. Accelerated and regional evolution of snake venom gland isozymes. Perspectives in Molecular Toxinology 2002, 387-400. John Wiley & Sons, NY. A. Ménez (Ed.).
44. 2 from snake venom. Toxicon 2003, 42:841-854.
45. Priimagi A.F., Mizrokhi L.J., Ilyin Y.V. The Drosophila mobile element jockey belongs to LINEs and contains coding sequences homologous to some retroviral proteins. Gene 1988, 70:253-262.
46. Pungercar J., et al. Amino acid sequence of ammodytoxin C as deduced from cDNA. Nucleic Acids Res. 1989, 17:4367.
47. 2 from the venom of long-nosed viper (Vipera ammodytes). Toxicon 1991, 29:269-273.
48. 2 from bovine pancreas and Crotalus atrox venom. J. Biol. Chem. 1985, 260:11627-11634.
49. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
50. Sambrook J., Fritsh E.F., Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 2nd ed.
51. Sugano T., Kajikawa M., Okada N. Isolation and characterization of retrotransposition-competent LINEs from zebrafish. Gene 2006, 365:74-82.
52. 2 from Trimeresurus flavoviridis (Habu snake) venom at 1.5Å resolution. J. Biochem. (Tokyo) 1995, 117:730-740.
53. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
54. 2 from the venom of Taiwan habu (Trimeresurus mucrosquamatus). Biochem. J. 1995, 311:895-900.
55. 2 from Callosellasma rhodostoma venom gland cloning and sequencing of 10 of the cDNAs, three-dimensional modeling and chemical modification of the major isozyme. Eur. J. Biochem. 2000, 267:6684-6691.
56. 2 of bamboo viper (Trimeresurus stejnegeri): molecular characterization, geographic variations and evidence of multiple ancestries. Biochem. J. 2004, 377:215-223.
57. Udomkit A., Forbes S., Dalgleish G., Finnegan D.J. BS a novel LINE-like element in Drosophila melanogaster. Nucleic Acids Res. 1995, 23:1354-1358.
58. 2 of two primitive tree vipers Trimeresurus puniceus and Trimeresurus borneensis. FEBS J. 2005, 272:3015-3025.
59. Wuster W., Peppin L., Pook C.E., Walker D.E. A nesting of vipers: phylogeny and historical biogeography of the Viperidae (Squamata: Sepentes). Mol. Phylgen. Evol. 2008, 49:445-459.
60. 2 from Trimeresurus flavoviridis venom. Toxicon 2001, 39:1069-1076.
61. Yang Z. PAML: a program package for phylogenetic analyis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.
62. 2 with low activity, from the venom of Trimeresurus flavoviridis (Habu snake). Toxicon 1990, 28:43-54.
63. Zhang J. Evolution by gene duplication: an update. Trends Ecol. Evol. 2003, 18:292-298.