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Identification and characterization of CACTA transposable elements capturing gene fragments in maize

Chinese Science Bulletin volume 54, pages 642–651 (2009)Cite this article

Abstract

Transposable elements (TEs)-mediated gene sequence movement is thought to play an important role in genome expansion and origin of genes with novel functions. In this study, a gene, HGGT, involved in vitamin E synthesis was used in a case study to discover and characterize transposons carrying gene fragments in maize. A total of 69 transposons that are distributed across the 10 chromosomes and have an average length of 3689 bp were identified from the maize sequence database by using the BLAST search algorithm. Three of these carry gene fragments from the progenitor HGGT gene, while the rest (66) contain gene fragments from other cellular genes. Nine of the 69 transposons contain fragments derived from two locations in the genome. By querying the maize Expressed Sequence Tag (EST) database, we found that at least thirteen out of the 69 TEs had corresponding transcripts. More interestingly, two transposons that carry gene fragments from two different chromosomal loci could be expressed as chimeric transcripts.

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References

  1. Bennetzen J L. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol, 2000, 42: 251–269

    Article  Google Scholar 

  2. Bennetzen J L. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev, 2005, 15: 621–627

    Article  Google Scholar 

  3. Wessler S R. Phenotypic diversity mediated by the maize transposable elements Ac and Spm. Science, 1988, 242(4877): 399–405

    Article  Google Scholar 

  4. Feschotte C, Jiang N, Wessler S R. Plant transposable elements: where genetics meets genomics. Nat Rev Genet, 2002, 3: 329–341

    Article  Google Scholar 

  5. Peterson P A. A mutable pale green locus in maize. Genetics, 1953, 38: 682–683

    Google Scholar 

  6. McClintock B. Mutations in maize and chromosomal aberrations in Neurospora. Carnegie Inst Washington Year Book, 1954, 53: 254–260

    Google Scholar 

  7. Chopra S, Brendel V, Zhang J, et al. Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor. Proc Natl Acad Sci USA, 1999, 96(26): 15330–15335

    Article  Google Scholar 

  8. Motohashi R, Ohtsubo E, Ohtsubo H. Identification of Tnr3, a suppressor-mutator/enhancer-like transposable element from rice. Mol Gen Genet, 1996, 250(2): 148–152

    Google Scholar 

  9. Zabala G, Vodkin L O. The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily. Plant Cell, 2005, 17: 2619–2632

    Article  Google Scholar 

  10. Tian P F. Progress in plant CACTA elements. Acta Genetica Sinica, 2006, 33(9): 765–774

    Article  Google Scholar 

  11. Gierl A, Lutticke S, Saedler H. TnpA product encoded by the transposable element En-1 of Zea mays is a DNA binding protein. EMBO J, 1988, 7(13): 4045–4053

    Google Scholar 

  12. Peterson P A. A relationship between the Spm and En control systems in maize. Am Nat, 1965, 99(908): 391–398

    Article  Google Scholar 

  13. Pereira A, Schwarz-Sommer Z, Gierl A, et al. Genetic and molecular analysis of the Enhancer (En) transposable element system of Zea mays. EMBO J, 1985, 4(1): 17–23

    Google Scholar 

  14. Gierl A, Schwarz-Sommer Z, Saedler H. Molecular interactions between the components of the En-I transposable element system of Zea mays. EMBO J, 1985, 4(3): 579–583

    Google Scholar 

  15. Pereira A, Cuypers H, Gierl A, et al. Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J, 1986, 5(5): 835–841

    Google Scholar 

  16. Masson P, Surosky R, Kingsbury J A, et al. Genetic and molecular analysis of the Spm-dependent a-m2 alleles of the maize a locus. Genetics, 1987, 177: 117–137

    Google Scholar 

  17. Talbert L E, Chandler V L. Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol Biol Evol, 1988, 5(5): 519–529

    Google Scholar 

  18. Jiang N, Bao Z, Zhang X, et al. Pack-MULE transposable elements mediate gene evolution in plants. Nature, 2004, 431: 569–573

    Article  Google Scholar 

  19. Ohtsu K, Hirano H Y, Tsutsumi N, et al. Anaconda, a new class of transposon belonging to the Mu superfamily, has diversified by acquiring host genes during rice evolution. Mol Genet Genomics, 2005, 274: 606–615

    Article  Google Scholar 

  20. Juretic N, Hoen D R, Huynh M L, et al. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res, 2005, 15: 1292–1297

    Article  Google Scholar 

  21. Hoen D R, Park K C, Elrouby N, et al. Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol, 2006, 23(6): 1254–1268

    Article  Google Scholar 

  22. Holligan D, Zhang X, Jiang N, et al. The transposable element landscape of the model legume Lotus japonicus. Genetics, 2006, 174: 2215–2228

    Article  Google Scholar 

  23. Leeuwen H V, Monfort A, Puigdomenech P. Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains. Mol Genet Genomics, 2007, 277: 357–364

    Article  Google Scholar 

  24. Gupta S, Gallavotti A, Stryker G A, et al. A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol Biol, 2005, 57: 115–127

    Article  Google Scholar 

  25. Lai J, Li Y, Messing J, et al. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci USA, 2005, 102: 9068–9073

    Article  Google Scholar 

  26. Morgante M, Brunner S, Pea G, et al. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet, 2005, 37(9): 997–1002

    Article  Google Scholar 

  27. Takahashi S, Inagaki Y, Satoh H, et al. Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory. Mol Gen Genet, 1999, 261: 447–451

    Article  Google Scholar 

  28. Kawasaki S, Nitasaka E. Characterization of Tpn1 family in the Japanese morning glory: En/Spm-related transposable elements capturing host genes. Plant Cell Physiol, 2004, 45(7): 933–944

    Article  Google Scholar 

  29. Roccaro M, Li Y, Sommer H, et al. ROSINA (RSI) is part of a CACTA transposable element, TamRSI, and links flower development to transposon activity. Mol Genet Genomics, 2007, 278: 243–254

    Article  Google Scholar 

  30. Kohany O, Gentles A J, Hankus L, et al. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, 2006, 25(7): 474

    Article  Google Scholar 

  31. Edgar R C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acid Res, 2004, 32(5): 1792–1797

    Article  Google Scholar 

  32. Hall T A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp, 1999, 41: 95–98

    Google Scholar 

  33. Felsenstein J. PHYLIP (Phylongeny Inference Package), version 3.6. (Department of Genetics, University of Washington, Seattle, 2000)

    Google Scholar 

  34. Kumar S, Tamura K, Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform, 2004, 5(2): 150–163

    Article  Google Scholar 

  35. Cahoon E B, Hall S E, Ripp K G, et al. Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content. Nat Biotechnol, 2003, 21: 1082–1087

    Article  Google Scholar 

  36. Frey M, Reinecke J, Grant S, et al. Excision of the En/Spm transposable element of Zea mays requires two element-encoded proteins. EMBO J, 1990, 9(12): 4037–4044

    Google Scholar 

  37. Bercury S D, Panavas T, Irenze K, et al. Molecular analysis of the Doppia transposable element of maize. Plant Mol Biol, 2001, 47: 341–351

    Article  Google Scholar 

  38. Yim Y S, Davis G L, Duru N A, et al. Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization. Plant Physiol, 2002, 130: 1686–1696

    Article  Google Scholar 

  39. Jameson N, Georgelis N, Fouladbash E, et al. Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize. Plant Mol Biol, 2008, 67: 295–304

    Article  Google Scholar 

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Authors and Affiliations

  1. National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China

    Qing Li, Lin Li, JingRui Dai, JianSheng Li & JianBing Yan

  2. International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, 06600, Mexico

    JianBing Yan

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  1. Qing Li
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  2. Lin Li
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  3. JingRui Dai
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  4. JianSheng Li
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  5. JianBing Yan
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Corresponding author

Correspondence to JianBing Yan.

Additional information

Supported by National Natural Science Foundation of China (Grant No. 30500322) and National Hi-Tech Research and Development Program of China (Grant Nos. 2006AA10Z183, 2006AA10A107)

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Li, Q., Li, L., Dai, J. et al. Identification and characterization of CACTA transposable elements capturing gene fragments in maize. Chin. Sci. Bull. 54, 642–651 (2009). https://doi.org/10.1007/s11434-009-0061-2

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  • DOI: https://doi.org/10.1007/s11434-009-0061-2

Keywords

  • CACTA elements
  • gene fragment
  • genome distribution
  • chimeric transcripts
  • maize