Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: The key for their pattern of distribution within and across plants?

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Bousios, Alexandros ^a   Darzentas, Nikos ^b   Tsaftaris, Athanasios ^b,c   Pearce, Stephen R ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b INFORMATION TECHNOLOGIES INSTITUTE   (Greece)

^c ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE STUDY; COMPUTER ANALYSIS; CONTROLLED STUDY; CPG ISLAND; GENE STRUCTURE; GENETIC VARIABILITY; GENOME SIZE; INVERTED REPEAT; LONG TERMINAL REPEAT; NONHUMAN; PLANT VIRUS; PROMOTER REGION; PROTEIN MOTIF; PSEUDOVIRIDAE; RETROPOSON; SEQUENCE ALIGNMENT; SIREVIRUS; VIROGENESIS; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS TRANSMISSION; ALGORITHM; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETICS; NUCLEOTIDE SEQUENCE; PLANT; TATA BOX; VIROLOGY;

EUKARYOTA;

VIRUS DNA;

ALGORITHMS; COMPARATIVE GENOMIC HYBRIDIZATION; CONSERVED SEQUENCE; CPG ISLANDS; DNA, VIRAL; GENOME, VIRAL; PLANT VIRUSES; PLANTS; RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TATA BOX;

EID: 77649108099     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-89     Document Type: Article

References (66)

1. Hansen C, Heslop-Harrison JS. Sequences and phylogenies of plant pararetroviruses, viruses, and transposable elements. Advances in Botanical Research Incorporating Advances in Plant Pathology 2004, 41:165-193.
2. Kumar A, Bennetzen JL. Plant retrotransposons. Annu Rev Genet 1999, 33:479-532. 10.1146/annurev.genet.33.1.479, 10690416.
3. Bousios A, Saldana-Oyarzabal I, Valenzuela-Zapata AG, Wood C, Pearce SR. Isolation and characterization of Ty1-copia retrotransposon sequences in the blue agave (Agave tequilana Weber var. azul) and their development as SSAP markers for phylogenetic analysis. Plant Science 2007, 172(2):291-298.
4. Feschotte C, Jiang N, Wessler SR. Plant transposable elements: Where genetics meets genomics. Nature Reviews Genetics 2002, 3(5):329-341. 10.1038/nrg793, 11988759.
5. Pearce SR, Harrison G, HeslopHarrison PJS, Flavell AJ, Kumar A. Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale). Genome 1997, 40(5):617-625. 10.1139/g97-081, 9352643.
6. Vitte C, Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenetic and Genome Research 2005, 110(1-4):91-107. 10.1159/000084941, 16093661.
7. Pereira V. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol 2004, 5(10):R79. 10.1186/gb-2004-5-10-r79, 545599, 15461797.
8. McCarthy EM, Liu J, Lizhi G, McDonald JF. Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 2002, 3(10):RESEARCH0053. 10.1186/gb-2002-3-10-research0053, 134482, 12372141.
9. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, SanMiguel PJ, Bennetzen JL. Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome. Plos Genetics 2009, 5(11):e1000732. 10.1371/journal.pgen.1000732, 2774510, 19936065.
10. Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009, 326(5956):1112-1115. 10.1126/science.1178534, 19965430.
11. Vicient CM, Suoniemi A, Anamthamat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 1999, 11(9):1769-1784. 10.1105/tpc.11.9.1769, 144304, 10488242.
12. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 2007, 8(12):973-982. 10.1038/nrg2165, 17984973.
13. Peterson-Burch BD, Voytas DF. Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol 2002, 19(11):1832-1845.
14. Grandbastien MA, Lucas H, Morel JB, Mhiri C, Vernhettes S, Casacuberta JM. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica 1997, 100(1-3):241-252. 10.1023/A:1018302216927, 9440277.
15. Vernhettes S, Grandbastien MA, Casacuberta JM. In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1. Plant Molecular Biology 1997, 35(5):673-679. 10.1023/A:1005826605598, 9349289.
16. Wilhelm M, Wilhelm FX. Reverse transcription of retroviruses and LTR retrotransposons. Cellular and Molecular Life Sciences 2001, 58(9):1246-1262. 10.1007/PL00000937, 11577982.
17. Boeke JD, Eickbush TH, Sandmeyer SB, Voytas DF. Index of Viruses - Pseudoviridae (2006). ICTVdB - The Universal Virus Database, version 4 2006, Columbia University, New York, USA, Buchen-Osmond C.
18. Havecker ER, Gao X, Voytas DF. The sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain. Plant Physiol 2005, 139(2):857-868. 10.1104/pp.105.065680, 1256001, 16183843.
19. Havecker ER, Gao X, Voytas DF. The diversity of LTR retrotransposons. Genome Biol 2004, 5(6):225. 10.1186/gb-2004-5-6-225, 463057, 15186483.
20. Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF. Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA-Publ RNA Soc 2003, 9(12):1422-1430.
21. Nagaki K, Song JQ, Stupar RM, Parokonny AS, Yuan QP, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang JM. Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 2003, 163(2):759-770. 1462457, 12618412.
22. Holligan D, Zhang XY, Jiang N, Pritham EJ, Wessler SR. The transposable element landscape of the model legume Lotus japonicus. Genetics 2006, 174(4):2215-2228. 10.1534/genetics.106.062752, 1698628, 17028332.
23. Kenward KD, Bai D, Ban MR, Brandle JE. Isolation and characterization of Tnd-1, a retrotransposon marker linked to black root rot resistance in tobacco. Theor Appl Genet 1999, 98(3-4):387-395.
24. Xiong Y, Eickbush TH. Origin and Evolution of Retroelements Based Upon Their Reverse-Transcriptase Sequences. Embo J 1990, 9(10):3353-3362. 552073, 1698615.
25. Rigoutsos I, Floratos A. Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 1998, 14(1):55-67. 10.1093/bioinformatics/14.1.55, 9520502.
26. Goff SP. Genetics of Retroviral Integration. Annu Rev Genet 1992, 26:527-544. 10.1146/annurev.ge.26.120192.002523, 1482125.
27. Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 1999, 27(1):297-300. 10.1093/nar/27.1.297, 148163, 9847208.
28. Gardiner-Garden M, Frommer M. Cpg Islands in Vertebrate Genomes. Journal of Molecular Biology 1987, 196(2):261-282. 10.1016/0022-2836(87)90689-9, 3656447.
29. Ashikawa I. Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. Plant J 2001, 26(6):617-625. 10.1046/j.1365-313x.2001.01062.x, 11489175.
30. Ashikawa I, Numa H, Sakata K. Segmental distribution of genes harboring a CpG island-like region on rice chromosomes. Molecular Genetics and Genomics 2006, 275(1):18-25. 10.1007/s00438-005-0060-1, 16283384.
31. Grace ML, Chandrasekharan MB, Hall TC, Crowe AJ. Sequence and spacing of TATA box elements are critical for accurate initiation from the beta-phaseolin promoter. J Biol Chem 2004, 279(9):8102-8110. 10.1074/jbc.M309376200, 14660650.
32. Wang H, Liu JS. LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics 2008, 9.
33. Bugreev DV, Baranova S, Zakharova OD, Parissi V, Desjobert C, Sottofattori E, Balbi A, Litvak S, Tarrago-Litvak L, Nevinsky GA. Dynamic, thermodynamic, and kinetic basis for recognition and transformation of DNA by human immunodeficiency virus type 1 integrase. Biochemistry 2003, 42(30):9235-9247. 10.1021/bi0300480, 12885259.
34. Wicker T, Keller B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Research 2007, 17:1072-1081. 10.1101/gr.6214107, 1899118, 17556529.
35. Wright DA, Voytas DF. Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Research 2002, 12(1):122-131. 10.1101/gr.196001, 155253, 11779837.
36. Bowman EH, Pathak VK, Hu WS. Efficient initiation and strand transfer of polypurine tract-primed plus-strand DNA prevent strand transfer of internally initiated plus-strand DNAs. Journal of Virology 1996, 70(3):1687-1694. 189992, 8627689.
37. Heyman T, Agoutin B, Friant S, Wilhelm FX, Wilhelm ML. Plus-Strand DNA-Synthesis of the Yeast Retrotransposon Ty1 Is Initiated at 2 Sites, Ppt1 Next to the 3'-Ltr and Ppt2 within the Pol Gene - Ppt1 Is Sufficient for Ty1 Transposition. Journal of Molecular Biology 1995, 253(2):291-303. 10.1006/jmbi.1995.0553, 7563090.
38. Friant S, Heyman T, Wilhelm FX, Wilhelm M. Role of RNA primers in initiation of minus-strand and plus-strand DNA synthesis of the yeast retrotransposon Ty1. Biochimie 1996, 78(7):674-680. 10.1016/S0300-9084(96)80013-7, 8955910.
39. Charneau P, Alizon M, Clavel F. A 2nd Origin of DNA Plus-Strand Synthesis Is Required for Optimal Human-Immunodeficiency-Virus Replication. Journal of Virology 1992, 66(5):2814-2820. 241038, 1560526.
40. Wilson S, Matyunina LV, McDonald JF. An enhancer-region within the copia untranslated leader contains binding sites for Drosophila regulatory proteins. Gene 1998, 209(1-2):239-246. 10.1016/S0378-1119(98)00048-1, 9524274.
41. Moates JM, Magnuson MA. The Pal elements in the upstream glucokinase promoter exhibit dyad symmetry and display cell-specific enhancer activity when multimerised. Diabetologia 2004, 47(9):1632-1640. 10.1007/s00125-004-1497-1, 15365616.
42. Peterson-Burch BD, Wright DA, Laten HM, Voytas DF. Retroviruses in plants?. Trends in Genetics 2000, 16(4):151-152. 10.1016/S0168-9525(00)01981-8, 10729827.
43. Vicient CM, Kalendar R, Schulman AH. Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Research 2001, 11(12):2041-2049. 10.1101/gr.193301, 311225, 11731494.
44. Havecker ER, Voytas DE. The soybean retroelement SIRE1 uses stop codon suppression to express its envelope-like protein. EMBO Rep 2003, 4(3):274-277. 10.1038/sj.embor.embor773, 1315901, 12634845.
45. Brill LM, Nunn RS, Kahn TW, Yeager M, Beachy RN. Recombinant tobacco mosaic virus movement protein is an RNA-binding, alpha-helical membrane protein. Proc Natl Acad Sci USA 2000, 97(13):7112-7117. 10.1073/pnas.130187897, 16508, 10840061.
46. Melcher U. The '30K' superfamily of viral movement proteins. Journal of General Virology 2000, 81:257-266.
47. Casacuberta JM, Vernhettes S, Audeon C, Grandbastien MA. Quasispecies in retrotransposons: a role for sequence variability in Tnt1 evolution. Genetica 1997, 100(1-3):109-117. 10.1023/A:1018309007841, 9440263.
48. Manetti ME, Rossi M, Costa APP, Clausen AM, Van Sluys MA. Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera. BMC Evol Biol 2007, 7. 10.1186/1471-2148-7-34, 1838419, 17343755.
49. Beguiristain T, Grandbastien MA, Puigdomenech P, Casacuberta JM. Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants. Plant Physiol 2001, 127(1):212-221. 10.1104/pp.127.1.212, 117977, 11553749.
50. Costa APP, Scortecci KC, Hashimoto RY, Araujo PG, Grandbastien MA, Van Sluys MA. Retrolyc1-1, a member of the Tnt1 retrotransposon super-family in the Lycopersicon peruvianum genome. Genetica 1999, 107(1-3):65-72.
51. Araujo PG, Casacuberta JM, Costa APP, Hashimoto RY, Grandbastien MA, Van Sluys MA. Retrolyc1 subfamilies defined by different U3 LTR regulatory regions in the Lycopersicon genus. Molecular Genetics and Genomics 2001, 266(1):35-41. 10.1007/s004380100514, 11589575.
52. Vernhettes S, Grandbastien MA, Casacuberta JM. The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high variability of its regulatory sequences. Mol Biol Evol 1998, 15(7):827-836.
53. Chaw SM, Chang CC, Chen HL, Li WH. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 2004, 58(4):424-441. 10.1007/s00239-003-2564-9, 15114421.
54. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 2009, 41(5):563-571. 10.1038/ng.368, 19377475.
55. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nature Reviews Genetics 2009, 10(3):155-159. 10.1038/nrg2521, 19188922.
56. Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics 2007, 8(4):272-285. 10.1038/nrg2072, 17363976.
57. Feschotte C. Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics 2008, 9(5):397-405. 10.1038/nrg2337, 2596197, 18368054.
58. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31(13):3497-3500. 10.1093/nar/gkg500, 168907, 12824352.
59. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25(9):1189-1191. 10.1093/bioinformatics/btp033, 2672624, 19151095.
60. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
61. Saitou N, Nei M. The Neighbor-Joining Method - a New Method for Reconstructing Phylogenetic Trees. Mol Biol Evol 1987, 4(4):406-425.
62. Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. Evolving Genes and Proteins 1965, 97-166. Academic Press, New York, Bryson V, Vogel HJ.
63. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27(2):573-580. 10.1093/nar/27.2.573, 148217, 9862982.
64. Gelfand Y, Rodriguez A, Benson G. TRDB - The Tandem Repeats Database. Nucleic Acids Res 2007, 35:D80-D87. 10.1093/nar/gkl1013, 1781109, 17175540.
65. Prestridge DS. SIGNAL SCAN - A COMPUTER-PROGRAM THAT SCANS DNA-SEQUENCES FOR EUKARYOTIC TRANSCRIPTIONAL ELEMENTS. Computer Applications in the Biosciences 1991, 7(2):203-206.
66. Larsen F, Gundersen G, Lopez R, Prydz H. Cpg Islands as Gene Markers in the Human Genome. Genomics 1992, 13(4):1095-1107. 10.1016/0888-7543(92)90024-M, 1505946.