Envelope-like retrotransposons in the plant kingdom: Evidence of their presence in gymnosperms (Pinus pinaster)

Journal of Molecular Evolution

Volumn 67, Issue 5, 2008, Pages 517-525

  Miguel, Célia ^a   Simões, Marta ^a   Oliveira, Maria Margarida ^a,b   Rocheta, Margarida ^a,c  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^b UNIVERSITY OF LISBON   (Portugal)

^c INSTITUTO SUPERIOR DE AGRONOMIA   (Portugal)

Author keywords

Envelope like; Gymnosperm; LTR retrotransposon; Pinus pinaster; Retrovirus; RNAseH

Indexed keywords

RIBONUCLEASE H;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE SEQUENCE; GYMNOSPERM; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PINUS PINASTER; RETROPOSON;

AMINO ACID SEQUENCE; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; GENE PRODUCTS, ENV; GENES, PLANT; MOLECULAR SEQUENCE DATA; PHYLOGENY; PINUS; PROTEIN STRUCTURE, TERTIARY; RETROELEMENTS; RETROVIRIDAE; RIBONUCLEASE H; SEQUENCE ALIGNMENT;

ANIMALIA; GYMNOSPERMAE; INVERTEBRATA; MAGNOLIOPHYTA; PINUS PINASTER;

EID: 55949130857     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9168-3     Document Type: Article

References (47)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 3 403 410
2. M Berenyi ST Gichuki J Schmidt K Burg 2002 Ty1-copia retrotransposon- based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato Theor Appl Genet 105 862 869
3. JD Boeke VG Corces 1989 Transcription and reverse transcription of retrotransposons Annu Rev Microbiol 43 403 434
4. Boeke JD, Stoye JP (1997) Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In: Coffin JM, Hughes SH, Varmus HE (eds) retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 343-436
5. F Chavanne D-X Zhang M-F Liaud R Cerff 1998 Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/gypsy family highly amplified in pea and other legume species Plant Mol Biol 37 363 375
6. S Desset C Conte P Dimitri V Calco B Dastugue C Vaury 1999 Mobilization of two retroelements, ZAM and Idefix, in a novel unstable line of Drosophila melanogaster Mol Biol Evol 16 54 66
7. Y Emori T Shiba S Kanaya S Inouye S Yuki K Saigo 1985 The nucleotide sequences of copia and copia-related RNA in Drosophila virus-like particles Nature 315 773 776
8. AJ Favell E Dunbar R Anderson SR Pearce R Hartley 1992 Ty-1 copia group retrotransposons are ubiquitous and heterogeneous in higher plants Nucleic Acids Res 20 3639 3644
9. N Friesen A Brandes J Heslop-Harrison 2001 Diversity, origin and distribution of retrotransposons in conifers Mol Biol Evol 18 1176 1188
10. SA Gallo CM Finnegan M Viard Y Raviv A Dimitrov SS Rawat A Puri S Durell R Blumenthal 2003 The HIV env-mediated fusion reaction Biochim Biophys Acta Biomembr 1614 36 50
11. P Gonzales HA Lessios 1999 Evolution of sea urchin retroviral-like (SURL) elements: evidence from 40 echinoid species Mol Biol Evol 16 938 952
12. K Hofmann W Stoffel 1993 TMbase-a database of membrane spanning proteins segments Biol Chem Hoppe-Seyler 374 166
13. P Horton K-J Park T Obayashi N Fujita H Harada CJ Adams-Collier K Nakai 2007 WoLF PSORT: protein localization predictor Nucleic Acids Res 35 W585 W587
14. R Hull 2001 Classifying reverse transcribing elements: a proposal and a challenge to the ICTV Arch Virol 146 2255 2261
15. IK Jordan LV Matyunina JF McDonald 1999 Evidence for the recent horizontal transfer of long terminal repeat retrotransposon Proc Natl Acad Sci USA 96 12621 12625
16. FJ Kim J-L Battini N Manel M Sitbon 2004 Emergence of vertebrate retroviruses and envelope capture Virology 318 183 191
17. A Konieczny DF Voytas MP Cummingst FM Ausubel 1991 A Superfamily of Arabidopsis thaliana Retrotransposons Genetics 127 801 809
18. A Kumar 1998 The evolution of plant retroviruses: moving to green pastures Trends Plant Sci 3 371 374
19. A Kumar JL Bennetzen 1999 Plant retrotransposons Annu Rev Genet 33 479 532
20. HM Laten A Majumdar EA Gaucher 1998 Sire-1, a copia Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein Proc Natl Acad Sci USA 95 6897 6902
21. HM Laten ER Havecker LM Farmer DF Voytas 2003 Sire1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young Mol Biol Evol 20 1222 1230
22. E Lerat P Capy 1999 Retrotransposons and retroviruses: analysis of the envelope gene Mol Biol Evol 16 1198 1207
23. HS Malik TH Eickbush 2001 Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses Genome Res 11 1187 1197
24. A Marco I Marín 2005 Retrovirus-like elements in plants Recent Res Dev Plant Sci 3 1 10
25. K Nakai M Kanehisa 1992 A knowledge base for predicting protein localization sites in eukaryotic cells Genomics 14 897 911
26. P Neumann D Pozárková A Koblízková J Macas 2005 PIGY, a new plant envelope-class LTR retrotransposon Mol Gen Genom 275 43 53
27. SR Pearce 2006 SIRE-1, a putative plant retrovirus is closely related to a legume Ty1-copia retrotransposon family Cell Mol Biol Lett 12 120 126
28. SR Pearce C Stuart-Rogers MR Knox A Kumar THN Ellis AJ Flavell 1999 Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies Plant J 19 711 717
29. T Pélissier S Tutois J-M Deragon S Tourmente S Genestier G Picard 1995 Athila, a new retroelement from Arabidopsis thaliana Plant Mol Biol 29 441 452
30. BD Peterson-Burch DA Wright HM Laten DF Voytas 2000 Retroviruses in plants? Trends Genet 16 151 152
31. Rabson AB, Graves BJ (1997) Synthesis and processing of viral RNA. In: Coffin JM, Hughes SH, Varmus HE (eds) Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 205-261
32. B Rost R Casadio P Fariselli C Sander 1995 Transmembrane helices predicted at 95% accuracy Prot Sci 4 521 533
33. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
34. Schulman AH, Flavell AJ, Ellis THN (2004) The application of LTR retrotransposons as genetic markers in plants. In: Capy W (ed) Mobile genetic elements: protocols and genomic applications. Humana Press, Totowa, NJ, pp 145-173
35. C Stuart-Rogers AJ Flavell 2001 The evolution of Ty1-copia group retrotransposons in gymnosperms Mol Biol Evol 18 155 163
36. A Suoniemi J Tanskanen AH Schlman 1998 Gypsy-like retrotransposon are widespread in the plant kingdom Plant J 13 699 705
37. Swanstrom R, Wills JW (1997) Synthesis, assembly, and processing of viral proteins. In: Coffin JM, Hughes SH, Varmus HE (eds) Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 263-334
38. NH Syed S Sureshsundar MJ Wilkinson BS Bhau JJV Cavalcanti AJ Flavell 2005 Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.) Theor Appl Genet 110 1195 1202
39. S Tanda JL Mullor VG Corces 1994 The Drosophila tom retrotransposon encodes an envelope protein Mol Cell Biol 14 5392 5401
40. van-Regenmortel MHV, Fauquet CM, Bishop DHL, Carsten EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR (2000) Virus taxonomy: seventh report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA
41. CM Vicient R Kalendar AH Schulman 2001 Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants Genome Res 11 2041 2049
42. Vogt VM (1997) Retroviral virions and genomes. In: Coffin JM, Hughes SH, Varmus HE (eds) Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 27-69
43. P Vos R Hogers M Bleeker M Reijans Lee Tvd M Hornes A Frijters J Pot J Peleman M Kuiper M Zabeau 1995 AFLP: a new technique for DNA fingerprinting Nucleic Acids Res 23 4407 4414
44. DA Wright DF Voytas 1998 Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins Genetics 149 703 715
45. DA Wright DF Voytas 2001 Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses Genome Res 12 122 131
46. Y Xiong TH Eickbush 1990 Origin and evolution of retroelements based on their reverse transcriptase sequences EMBO J 9 3353 3362
47. ST Yano B Panbehi A Das HM Laten 1990 Diaspora, a large family of Ty3-gypsy retrotransposons in Glycine max, is an envelope-less member of an endogenous plant retrovirus lineage BMC Evol Biol 5 1 14