Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

Mobile DNA

Volumn 1, Issue 1, 2010, Pages

  Bao, Weidong ^a   Kapitonov, Vladimir V ^a   Jurka, Jerzy ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; INTEGRASE; PROTEINASE;

AMINO TERMINAL SEQUENCE; APHID; APLYSIA; ARTICLE; CARBOXY TERMINAL SEQUENCE; COELENTERATE; EUKARYOTE; EVOLUTIONARY ALGORITHM; GENE DUPLICATION; GINGER1; GINGER2; HUMAN; LONG TERMINAL REPEAT; MALASSEZIA GLOBOSA; NONHUMAN; OVARY TUMOR; PHYLOGENY; PRIORITY JOURNAL; RETROPOSON; RETROVIRUS; SEA ANEMONE; SNAIL; TRANSPOSON; TRICHINELLA SPIRALIS; TRICHOMONAS VAGINALIS;

BACTERIA (MICROORGANISMS); EUKARYOTA; VERTEBRATA; ZINGIBER OFFICINALE;

EID: 77956352772     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-1-3     Document Type: Article

References (45)

1. Origins and evolution of retrotransposons. T Eickbush H Malik, Mobile DNA II Washington, DC, USA: American Society for Microbiology Press, Craig NL, Craigie R, Gellert M, Lambowitz AM, 2002 1111 1144
2. A unified classification system for eukaryotic transposable elements. T Wicker F Sabot A Hua-Van JL Bennetzen P Capy B Chalhoub A Flavell P Leroy M Morgante O Panaud E Paux P SanMiguel AH Schulman, Nat Rev Genet 2007 8 973 982 10.1038/nrg2165 17984973
3. A universal classification of eukaryotic transposable elements implemented in Repbase. VV Kapitonov J Jurka, Nat Rev Genet 2008 9 411 412 10.1038/nrg2165-c1 18421312
4. Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. TJ Goodwin MI Butler RT Poulter, Microbiology 2003 149 3099 3109 10.1099/mic.0.26529-0 14600222
5. First cryptons from invertebrates. J Jurka VV Kapitonov, Repbase Rep 2008 8 232 233
6. First cryptons from insects. J Jurka, Repbase Rep 2009 9 480 480
7. First cryptons from insects. J Jurka, Repbase Rep 2009 9 673 673
8. New superfamilies of eukaryotic DNA transposons and their internal divisions. W Bao MG Jurka VV Kapitonov J Jurka, Mol Biol Evol 2009 26 983 993 10.1093/molbev/msp013 19174482
9. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? O Fayet P Ramond P Polard MF Prere M Chandler, Mol Microbiol 1990 4 1771 1777 10.1111/j.1365-2958.1990.tb00555.x 1963920
10. Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor? P Capy R Vitalis T Langin D Higuet C Bazin, J Mol Evol 1996 42 359 368 10.1007/BF02337546 8661997
11. Insertion sequences revisited. M Chandler J Mahillon, Mobile DNA II Washington, DC, USA: American Society for Microbiology Press, Craig NL, Craigie R, Gellert M, Lambowitz AM, 2002 305 366
12. Do the integrases of LTR-retrotransposons and class II element transposases have a common ancestor? P Capy T Langin D Higuet P Maurer C Bazin, Genetica 1997 100 63 72 10.1023/A:1018300721953 9440259
13. Acquisition/loss of modules: the construction set of transposable elements. P Capy C Maisonhaute, Russian J Genet 2002 38 594 601 10.1023/A:1016027530962
14. Tdd-4, a DNA transposon of Dictyostelium that encodes proteins similar to LTR retroelement integrases. DJ Wells, Nucleic Acids Res 1999 27 2408 2415 10.1093/nar/27.11.2408 10325432
15. The complex repeats of Dictyostelium discoideum. G Glockner K Szafranski T Winckler T Dingermann MA Quail E Cox L Eichinger AA Noegel A Rosenthal, Genome Res 2001 11 585 594 10.1101/gr.GR-1622RR 11282973
16. Self-synthesizing DNA transposons in eukaryotes. VV Kapitonov J Jurka, Proc Natl Acad Sci USA 2006 103 4540 4545 10.1073/pnas.0600833103 16537396
17. The GP(Y/F) domain of TF1 integrase multimerizes when present in a fragment, and substitutions in this domain reduce enzymatic activity of the full-length protein. H Ebina AG Chatterjee RL Judson HL Levin, J Biol Chem 2008 283 15965 15974 10.1074/jbc.M801354200 18397885
18. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. HS Malik TH Eickbush, J Virol 1999 73 5186 5190 10233986
19. Analysis of canonical and non-canonical splice sites in mammalian genomes. M Burset IA Seledtsov VV Solovyev, Nucleic Acids Res 2000 28 4364 4375 10.1093/nar/28.21.4364 11058137
20. The Gypsy Database (GyDB) of mobile genetic elements. C Llorens R Futami D Bezemer A Moya, Nucleic Acids Res 2008 36 38 46 10.1093/nar/gkm697 17895280
21. Relationships of gag-pol diversity between Ty3/Gypsy and retroviridae LTR retroelements and the three kings hypothesis. C Llorens MA Fares A Moya, BMC Evol Biol 2008 8 276 10.1186/1471-2148-8-276 18842133
22. A mammalian gene evolved from the integrase domain of an LTR retrotransposon. C Llorens I Marin, Mol Biol Evol 2001 18 1597 1600 11470852
23. DIRS-1 and the other tyrosine recombinase retrotransposons. RT Poulter TJ Goodwin, Cytogenet Genome Res 2005 110 575 588 10.1159/000084991 16093711
24. Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. C Vitte O Panaud, Mol Biol Evol 2003 20 528 540 10.1093/molbev/msg055 12654934
25. Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. SA Chow KA Vincent V Ellison PO Brown, Science 1992 255 723 726 10.1126/science.1738845 1738845
26. MuDr-type DNA transposons from Hydra magnipapillata. W Bao J Jurka, Repbase Rep 2008 8 2075 2075
27. MuDr-type DNA transposons from Branchiostoma floridae. W Bao J Jurka, Repbase Rep 2009 9 683 683
28. VANDAL20, a family of monstrous MuDR-like DNA transposons. VV Kapitonov J Jurka, Repbase Rep 2001 1 31 31
29. Transposon-mediated expansion and diversification of a family of ULP-like genes. DR Hoen KC Park N Elrouby Z Yu N Mohabir RK Cowan TE Bureau, Mol Biol Evol 2006 23 1254 1268 10.1093/molbev/msk015 16581939
30. MuDR-type DNA transposon from maize. W Bao J Jurka, Repbase Rep 2008 8 739 739
31. Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains. H van Leeuwen A Monfort P Puigdomenech, Mol Genet Genomics 2007 277 357 364 10.1007/s00438-006-0194-9 17136348
32. Helitron-1-SP, a family of autonomous Helitrons in the sea urchin genome. VV Kapitonov J Jurka, Repbase Rep 2005 5 393 393
33. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. E Mossessova CD Lima, Mol Cell 2000 5 865 876 10.1016/S1097-2765(00)80326-3 10882122
34. Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. TE Messick NS Russell AJ Iwata KL Sarachan R Shiekhattar JR Shanks FE Reyes-Turcu KD Wilkinson R Marmorstein, J Biol Chem 2008 283 11038 11049 10.1074/jbc.M704398200 18270205
35. A single-copy IS5-like transposon in the genome of a bdelloid rotifer. EA Gladyshev IR Arkhipova, Mol Biol Evol 2009 26 1921 1929 10.1093/molbev/msp104 19443853
36. Principles of ubiquitin and SUMO modifications in DNA repair. S Bergink S Jentsch, Nature 2009 458 461 467 10.1038/nature07963 19325626
37. Repbase update, a database of eukaryotic repetitive elements. J Jurka VV Kapitonov A Pavlicek P Klonowski O Kohany J Walichiewicz, Cytogenet Genome Res 2005 110 462 467 10.1159/000084979 16093699
38. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
39. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucl Acids Symp Ser 1999 41 95 98
40. WebLogo: a sequence logo generator. GE Crooks G Hon JM Chandonia SE Brenner, Genome Res 2004 14 1188 1190 10.1101/gr.849004 15173120
41. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
42. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
43. CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. YA Bae SY Moon Y Kong SY Cho MG Rhyu, Mol Biol Evol 2001 18 1474 1483 11470838
44. A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. EA Gladyshev M Meselson IR Arkhipova, Gene 2007 390 136 145 10.1016/j.gene.2006.09.025 17129685
45. Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis. S Peddigari W Zhang K Takechi H Takano S Takio, Gene 2008 424 153 158 10.1016/j.gene.2008.07.021 18708130