GIN transposons: Genetic elements linking retrotransposons and genes

Molecular Biology and Evolution

Volumn 27, Issue 8, 2010, Pages 1903-1911

  Marín, Ignacio ^a  

^a INSTITUTO DE BIOMEDICINA DE VALENCIA   (Spain)

Author keywords

cysteine protease; DNA transposon; integrase; otubain; retrotransposon; selfish DNA

Indexed keywords

DNA; INTEGRASE; RETROPOSON; TRANSPOSON;

ARTICLE; GENE; GENE SEQUENCE; GENE STRUCTURE; GIN1 GENE; GIN2 GENE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PHYLOGENY; RETROPOSON; TRANSPOSON; VERTEBRATE; AMINO ACID SEQUENCE; ANIMAL; CLASSIFICATION; EVOLUTION; GENETICS; HUMAN; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; EVOLUTION; GENES; HUMANS; INTEGRASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; BIOLOGICAL EVOLUTION;

ANIMALIA; CHORDATA; VERTEBRATA;

EID: 77954995063     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq072     Document Type: Article

References (37)

1. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
2. Brandt J, Schrauth S, Veith AM, Froschauer A, Haneke T, Schultheis C, Gessler M, Leimeister C, Volff JN. 2005. Transpos-able elements as a source of genetic innovation: expression and evolution of a family of retrotransposon- derived neogenes in mammals. Gene 345:101-111.
3. Campillos M, Doerks T, Shah PK, Bork P. 2006. Computational characterization of multiple Gag-like human proteins. Trends Genet. 22:585-589.
4. Dooner HK, Weil CF. 2007. Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev. 17:486-492.
5. Dwivedi B, Gadagkar SR. 2009. Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol Biol. 9:211.
6. Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 9:397-405.
7. Feschotte C, Pritham EJ. 2005. Non-mammalian c-integrases are encoded by giant transposable elements. Trends Genet. 21:551-552.
8. Feschotte C, Pritham EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 41:331-368.
9. Gao X, Voytas DF. 2005. A eukaryotic gene family related to retroelement integrases. Trends Genet. 21:133-137.
10. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
11. Haren L, Ton-Hoang B, Chandler M. 1999. Integrating DNA: transposases and retroviral integrases. Annu Rev Microbiol. 53: 245-281.
12. Hay RT. 2007. SUMO-specific proteases: a twist in the tail. Trends Cell Biol. 17:370-376.
13. Hoen DR, Park KC, Elrouby N, Yu Z, Mohabir N, Cowan RK, Bureau TE. 2006. Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol. 23:1254-1268.
14. Hubbard TJP, Aken BL, Ayling S, et al. (58 co-authors). 2009. Ensembl 2009., Nucl Acids Res. 37:D690-D697.
15. Nucl Acids Res. 37:D690-D697. Jurka J, Kapitonov VV, Kohany O, Jurka MV. 2007. Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet. 8:241-259.
16. Kapitonov VV, Jurka J. 2006. Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci USA. 103:4540-4545.
17. Kim JH, Park KC, Chung SS, Band O, Chung CH. 2003. Deubiquitinat-ing enzymes as cellular regulators. J Biochem. 134:9-18.
18. Larkin MA, Blackshields G, Brown NP, et al. (13 co-authors). 2007. Clustal W and Clustal X version 2.
19. Bioinformatics 23: 2947-2948.
20. Lloréns C, Maŕn I. 2001. A mammalian gene evolved from the integrase domain of an LTR retrotransposon. Mol Biol Evol. 18:1597-1600.
21. Lynch C, Tristem M. 2003. A co-opted gypsy-type LTR-retrotrans-poson is conserved in the genomes of humans, sheep, mice and rats. Curr Biol. 13:1518-1523.
22. Marco A, Maŕn I. 2009. CGIN1: a retroviral contribution to mammalian genomes. Mol Biol Evol. 26:2167-2170.
23. Nanao MH, Tcherniuk SO, Chroboczek J, Dideberg O, Dessen A, Balakirev MY. 2004. Crystal structure of human otubain 2. EMBO Rep. 5:783-788.
24. Nicholas KB, Nicholas HB Jr. 1997. GeneDoc: a tool for editing and annotating multiple sequence alignments. [cited 2010 Jun 25] Available from: http://www.nrbsc.org/gfx/genedoc/index.html.
25. Ponting CP. 2008 The functional repertoires of metazoan genomes. Nat Rev Genet. 9:689-698.
26. Pritham EJ, Putliwala T, Feschotte C. 2007. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390:3-17.
27. Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ. 2008. MEROPS: the peptidase database. Nucl Acids Res. 36:D320-D325.
28. Swofford DL. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Version 4 Sunderland (MA): Sinauer Associates.
29. Sunderland (MA): Sinauer Associates. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4. Mol Biol Evol. 24:1596-1599.
30. Van Leeuwen H, Monfort A, Puigdomenech P. 2007. Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains. Mol Genet Genom. 277:357-364.
31. Venner S, Feschotte C, Biémont C. 2009. Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet. 25:317-323.
32. Volff JN. 2006. Turning junk into gold: domestication of transpos-able elements and the creation of new genes in eukaryotes. Bioessays 28:913-922.
33. Volff JN, Körting C, Schartl M. 2001. Ty3/Gypsy retrotransposon fossils in mammalian genomes: did they evolve into new cellular functions? Mol Biol Evol. 18:266-270.
34. Wells DJ. 1999. Tdd-4, a DNA transposon of Dictyostelium that encodes proteins similar to LTR retroelement integrases. Nucl Acids Res. 27:2408-2415.
35. Yeh RF, Lim LP, Burge CB. 2001. Computational inference of homologous gene structures in the human genome. Genome Res. 11:803-816.
36. Youngson NA, Kocialkowski S, Peel N, Ferguson-Smith AC. 2005. A small family of Sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. J Mol Evol. 61:481-490.
37. Zdobnov EM, Apweiler R. 2001. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847-848.