En-Spm-like transposons in Poaceae species: transposase sequence variability and chromosomal distribution

• Autorzy: Altinkut A , Raskina O. , Nevo E. , Belyayev A.
• Języki publikacji: EN

Abstrakty

EN

Belonging to Class II of transposable elements, En/Spm transposons are widespread in a variety of distantly related plant species. Here, we report on the sequence conservation of the transposase region from sequence analyses of En/Spm-like transposons from Poaceae species, namely Zingeria biebersteiniana, Zingeria trichopoda, Triticum monococcum, Triticum urartu, Hordeum spontaneum, and Aegilops speltoides. The transposase region of En/Spm-like transposons was cloned, sequenced, and compared with equivalent regions of Oryza and Arabidopsis from the gene bank database. Southern blot analysis indicated that the En/Spm transposon was present in low (Hordeum spontaneum, Triticum monococcum, Triticum urartu) through medium (Zingeria bieberstiana, Zingeria trichopoda) to relatively high (Aegilops speltoides) copy numbers in Poaceae species. A cytogenetic analysis of the chromosomal distribution of En/Spm transposons revealed the concurence of the chromosomal localization of the En/Spm clusters with mobile clusters of rDNA. An analysis of En/Spm-like transposase amino acid sequences was carried out to investigate sequence divergence between 5 genera — Triticum, Aegilops, Zingeria, Oryza and Arabidopsis. A distance matrix was generated; apparently, En/Spm-like transposase sequences shared the highest sequence homology intra-generically and, as expected, these sequences were significantly diverged from those of O. sativa and A. thaliana. A sequence comparison of En/Spm-like transposase coding regions defined that the intra-genomic complex of En/Spm-like transposons could be viewed as relatively independent, vertically transmitted, and permanently active systems inside higher plant genomes. The sequence data from this article was deposited in the EMBL/GenBank Data Libraries under the accession nos. AY707995-AY707996-AY707997-AY707998-AY707999-AY708000-AY708001-AY708002-AY708003-AY708004-AY708005-AY708005-AY265312.

Słowa kluczowe

EN

in situ hybridization; Aegilops speltoides; Triticum urartu; En-Spm transposon; Poaceae; plant genome; chromosome distribution; Triticum monococcum; Zingeria biebersteiniana; Zingeria trichopoda; plant species; En-Spm-like transposon; evolution; cereal; Hordeum spontaneum

• Wydawca: -
• Czasopismo: Cellular and Molecular Biology Letters
• Rocznik: 2006
• Tom: 11
• Numer: 2
• Opis fizyczny: p.214-229,fig.,ref.

Twórcy

autor

Altinkut A

• University of Haifa, Mt.Carmel, Haifa, 31905, Israel

autor

Raskina O.

autor

Nevo E.

autor

Belyayev A.

Bibliografia

• 1. Kumar, A. and Bennetzen, J.L. Plant retrotransposons. Annu. Rev. Genet. 33 (1999) 479-532.
• 2. Danilevskaya, O., Slot, F., Pavlova, M. and Pardue, M.L. Structure of the Drosophila HeT-A transposon: a retrotransposon-like element forming telomeres. Chromosoma 103 (1994) 215-224.
• 3. Gray, Y.H. It takes two transposons to tango: transposable-elementmediated chromosomal rearrangements. Trends Genet. 16 (2000) 461-468.
• 4. Kidwell, M.G. and Holyoake, A.J. Transposon-Induced Hotspots for Genomic Instability. Genome Res. 11 (2001) 1321-1322.
• 5. Xiong, Y. and Eickbush, T.H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9 (1990) 3353-3362.
• 6. Doolittle, R.F., Feng, D.F., Johnson, M.S. and Mclure, M.A. Origins and evolutionary relationships of retrovirus. Quarterly Rev. Biol. 64 (1989) 1-30.
• 7. Kunze, R., Saedler, H. and Lonnig, W. Plant transposable elements. Adv. Bot. Res. 27 (1997) 332-470.
• 8. Staginnus, C.B., Huettel, C.D., Schmidt, T. and Kahl, G. A PCR-based assay to detect En/Spm-like transposon sequences in plants. Chromosome Res. 9 (2001) 591-605.
• 9. Rhodes, P. and Vodkin, L. Organization of the Tgm family of transposable elements in soybean. Genetics 120 (1988) 597-604.
• 10. Shirsat, A. A transposon-like structure in the 5’ flanking sequence of the legumin gene from Pisum sativum. Mol. Genet. Genom. 212 (1988) 129- 133.
• 11. Nacken, W., Pietrowiak, R., Saedler, H. and Sommer, H. The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specifity of insertion. Mol. Genet. Genom. 228 (1991) 201-208.
• 12. Gierl, A. The En/Spm transposable element of maize. Curr. Topics Microbiol. Immunol. 204 (1996) 145-159.
• 13. Snowden, K. and Napoli, C. PsI: a novel Spm-like transposable element from Petunia hybrida. Plant J. 14 (1998) 43-54.
• 14. Aarts, M.G., Corzaan, P., Stiekema, W.J. and Pereira, A. A two-element Enhancer-Inhibitor transposon system in Arabidopsis thaliana. Mol. Gen. Genet 247 (1995) 555-564.
• 15. Wisman, E., Hartmann, U., Sagasser, M., Baumann, E., Palme, K., Hahlbrock, K., Saedler, H. and Weisshaar, B. Knock-out mutants from an En-1 mutagenized Arabidopsis thaliana population generate phenylpropanoid biosynthesis phenotypes. Proc. Natl. Acad. Sci. USA 95 (1998) 12432-12437.
• 16. Speulman, E., Metz, P.L.J., van Arkel, G., te Lintel Hekkert, B., Stiekma, W.J. and Pereira, A. A two-component Enhancer-Inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome. Plant Cell 11 (1999) 1853-1866.
• 17. Tissier, A.F., Marillonnet, S., Klimyuk, V., Patel, K., Angel Torres, M., Murphy, G. and Jones, J.D.G. Multiple Independent Defective Suppressormutator Transposon Insertions in Arabidopsis: A Tool for Functional Genomics. Plant Cell 11 (1999) 1841-1852.
• 18. Martinez, N.M., Greco, R., Van Arkel, G., Herrera-Estrella, L. And poson System in Arabidopsis. Plant Physiol. 129 (2002) 1544-1556.
• 19. Greco, R., Ouwerkerk, P.B.F., Taal, A.J.C., Sallaud, C., Guiderdoni, E., Meijer, A.H., Hoge, J.H.C. and Pereira., A. Transcription and somatic transposition of the maize En/Spm transposon system in rice. Mol. Gen. Genomics 270 (2004) 514-523.
• 20. Fedoroff, N.V. The Suppressor-mutator element and the evolutionary riddle of transposons. Genes Cells 4 (1999) 11-19.
• 21. Kidwell, K.K. and Osborn, T.C. Simple plant DNA isolation procedures. In: Plant Genomes: Methods for genetic and physical mapping. (Beckmann J.S. and Osborn T.C., Eds.), Kluwer Academic Publishers, 1992, 1-13.
• 22. Raskina, O., Belyayev, A. and Nevo, E. Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch. Chromosome Res. 12 (2004a) 153-161.
• 23. Altschul, S.F., Thomas, L.M., Alejandro, A.S., Jinghui, Z., Zheng, Z., Webb, M. and David, J.L. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402.
• 24. Pijnacker L.P. and Ferwerda, M.A. Giemsa C-banding of potato chromosomes. Can. J. Genet. Cytol. 26 (1984) 415-419.
• 25. Belyayev, A., Raskina, O. and Nevo, E. Chromosomal distribution of reverse transcriptase containing retroelements in two Triticeae species. Chromosome Res. 9 (2001) 129-136.
• 26. Taketa, S., Ando, H., Takeda, K., Harrison, G.E. and Heslop-Harrison, J.S. The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in genus Hordeum. Theor. Appl. Genet. 100 (2000) 169-176.
• 27. Raskina, O., Belyayev, A. and Nevo, E. Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA clusters variability in natural populations. Proc. Natl. Acad. Sci. USA 101 (2004b) 14818-14823.
• 28. Aragon-Alcaide, L., Miller, T., Schwarzacher, T., Reader, S. and Moore, G. A cereal centromere sequence. Chromosoma 105 (1996) 261-268.
• 29. Sumner, A.T. Chromosome banding and identification. in: Chromosome Analysis Protocols. (Gosden, J.R., Ed.,) Methods in Molecular Biology. Humana Press Inc., Totowa, NJ, 29 (1994) 83-96.
• 30. Giraldez, R., Cermeno, M.C. and Orellana, J. Comparison of C-banding pattern in chromosomes of inbred lines and open pollinated varieties of rye Secale cereale L. Z. Pflanzenzuecht 83 (1979) 40-48.
• 31. Kubis, S.E., Castilho, A.M.M.F., Vershinin, A.V. and Heslop-Harrison, J.S. Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol. Biol. 52 (2003) 69-79.
• 32. Saunders, V.A. and Houben, A. The pericentromeric heterochromatin of the grass Zingeria biebersteiniana (2n=4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences. Genome 44 (2001) 955-961.
• 33. Pearce, S.R., Pich, U., Harrison, G., Flavell, A.J., Heslop-Harrison, J.S., Schubert, I. and Kumar, A. The Ty1-copia group retrotransposons, a major component of Allium cepa genome, are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 4 (1996) 357-364.
• 34. Brandes, A., Heslop-Harrison, J.S., Kam, A., Kubis, S., Doudrick, R.L. and Schmidt, T. Comparative analysis of the chromosomal and genomic organization of Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol. Biol. 33 (1997) 11-21.
• 35. Lippman, Z., Gendrel, A.V., Black, M., Vaughn, W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D., Carrington, J.C., Doerge, R.W., Colot, V. and Martienssen, R. The role of RNA interference in heterochromatic silencing. Nature 431 (2004) 364-370.
• 36. Bennetzen, J. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42 (2000) 251-269.
• 37. Zhang, J. and Peterson, T. Genome rearrangements by nonlinear transposons in maize. Genetics 153 (1999) 1403-1410.
• 38. Ellis, T.H.N., Poyser, S.J, Knox, M.R., Vershinin, A.V. and Ambrose, M.J. Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol. Genet. Gen. 260 (1998) 9-19.
• 39. Fukuchi, A., Kikuchi, F. and Hirochika, H. DNA fingerprinting of cultivated rice with rice retrotransposon probes. Jpn. J. Genet. 68 (1993) 195-204.
• 40. Wolfe, K.H., Gouy, M., Yang, Y-W., Sharp, P.M. and Li, W-H. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86 (1989) 6201-6205.
• 41. Jacobs, B.F., Kingston, J.D. and Jacobs, L.L. The origin of grass-dominated ecosystems. Ann. Mo. Bot. Gard. 86 (1999) 590-643.