Transgene structures suggest that multiple mechanisms are involved in T-DNA integration in plants

Plant Science

Volumn 171, Issue 3, 2006, Pages 308-322

  Zhu, Qian Hao ^a,b   Ramm, Kerrie ^a,b   Eamens, Andrew L ^a   Dennis, Elizabeth S ^a,b   Upadhyaya, Narayana M ^a,b  

^a CSIRO   (Australia)

^b NSW DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

Author keywords

Filler DNA; Rice; T DNA integration; T DNA junction; Terminal microhomology

Indexed keywords

BACTERIA; DNA; GENETIC ENGINEERING;

FILLER DNA; T-DNA INTEGRATION; T-DNA JUNCTION; TERMINAL MICROHOMOLOGY;

PLANTS (BOTANY);

BACTERIA; GENETIC ENGINEERING; NUCLEIC ACIDS; RICE;

AGROBACTERIUM; RHIZOBIUM;

EID: 33745739881     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2006.03.019     Document Type: Article

References (42)

1. Stachel S.E., and Zambryski P.C. Bacteria-yeast conjugation. Generic trans-kingdom sex?. Nature 340 (1989) 190-191
2. Gelvin S.B. Agrobacterium and plant genes involved in T-DNA transfer and integration. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51 (2000) 223-256
3. Gelvin S.B. Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol. Mol. Biol. Rev. 67 (2003) 16-37
4. Hwang H.-H., and Gelvin S.B. Plant proteins that interact with VirB2, the Agrobacterium tumefaciens pilin protein, mediate plant transformation. Plant Cell 16 (2004) 3148-3167
5. Herrera-Estrella A., Chen Z.M., Van Montagu M., and Wang K. VirD proteins of Agrobacterium tumefaciens are required for the formation of a covalent DNA-protein complex at the 5′ terminus of T-strand molecules. EMBO J. 7 (1988) 4055-4062
6. Ballas N., and Citovsky V. Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Argobacterium VirD2 protein. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 10723-10728
7. Tzfira T., Vaidya M., and Citovsky V. VIP1, an Arabidopsis protein that interacts with Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. EMBO J. 20 (2001) 3596-3607
8. Tzfira T., Vaidya M., and Citovsky V. Involvement of targeted proteolysis in plant genetic transformation by Agrobacterium. Nature 431 (2004) 87-92
9. Chilton M.D., and Que Q. Targeted integration of T-DNA into the tobacco genome at double-stranded breaks: new insights on the mechanism of T-DNA integration. Plant Physiol. 133 (2003) 956-965
10. Tzfira T., Frankman L.R., Vaidya M., and Citovsky V. Site-specific integration of Agrobacterium tumefaciens T-DNA via double-stranded intermediates. Plant Physiol. 133 (2003) 1011-1023
11. Gheysen G., Villarroel R., and Montagu M. Illegitimate recombination in plants: a model for T-DNA integration. Genes Dev. 5 (1991) 287-297
12. Mayerhofer R., Koncz-Kalman Z., Nawrath C., Bakkeren G., Crameri A., Angelis K., Redei G.P., Schell J., Hohn B., and Koncz C. T-DNA integration: a mode of illegitimate recombination in plants. EMBO J. 10 (1991) 697-704
13. Tinland B. The integration of T-DNA into plant genomes. Trends Plant Sci. 1 (1996) 178-184
14. Köhler F., Cardon G., Pöhlman M., Gill R., and Schieder O. Enhamcement of transformation rates in higher plants by low-dose irradiation: are DNA repair systems involved in the incorporation of exogenous DNA into the plant genome?. Plant Mol. Biol. 12 (1989) 189-199
15. Salomon S., and Puchta H. Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO J. 17 (1998) 6086-6095
16. Kumar S., and Fladung M. Transgene integration in aspen: structures of integration sites and mechanism of T-DNA integration. Plant J. 31 (2002) 543-551
17. Gorbunova V.V., and Levy A.A. Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucleic Acids Res. 25 (1997) 4650-4657
18. De Buck S., Jacobs A., Van Montagu M., and Depicker A. The DNA sequences of T-DNA junctions suggest that complex T-DNA loci are formed by a recombination process resembling T-DNA integration. Plant J. 20 (1999) 295-304
19. De Neve M., De Buck S., Jacobs A., Van Montagu M., and Depicker A. T-DNA integration patterns in co-transformed plant cells suggest that T-DNA repeats originate from co-integration of separate T-DNAs. Plant J. 11 (1997) 15-29
20. De Block M., and Debrouwer D. Two T-DNAs co-transformed into Brassica napus by a double Agrobacterium tumefaciens infection are mainly integrated at the same locus. Theor. Appl. Genet. 82 (1991) 257-263
21. Kim S., Lee J., Jun S.H., Park S., Kang H.G., Kwon S., and An G. Transgene structures in T-DNA-inserted rice plants. Plant Mol. Biol. 52 (2003) 761-773
22. Windels P., De Buck S., Van Bockstaele E., De Loose M., and Depicker A. T-DNA integration in Arabidopsis chromosomes. Presence and origin of filler DNA sequences. Plant Physiol. 133 (2003) 2061-2068
23. Eamens A.L., Blanchard C.L., Dennis E.S., and Upadhyaya N.M. A bidirectional gene trap construct for T-DNA and Ds mediated insertional mutagenesis in rice (Oryza sativa L.). Plant Biotech. J. 2 (2004) 367-380
24. Tzfira T., Li J., Lacroix B., and Citovsky V. Agrobacterium T-DNA integration: molecules and models. Trends Genet. 20 (2004) 375-383
25. Upadhyaya N.M., Zhou X.-R., Zhu Q.-H., Ramm K., Wu L., Eamens A., Sivakumar R., Kato T., Yun D.-W., Kumar S., Narayanan K.K., Peacock W.J., and Dennis E.S. An iAc/Ds gene and enhancer trapping system for insertional mutagenesis in rice. Funct. Plant Biol. 29 (2002) 547-559
26. Upadhyaya N.M., Zhu Q.-H., Zhou X.-R., Hoque M.S., Ramm K., Shivakkumar S., Smith K.F., Pan S.-T., Li S.-Z., Peng K.-F., and Dennis E.S. Dissociation (Ds) constructs, mapped Ds launch pads and a transiently expressed transposase system suitable for targeted insertional mutagenesis in rice. Theor. Appl. Genet. 112 (2006) 1326-1341
27. Upadhyaya N.M., Surin B., Ramm K., Gaudron J., Schünmann P.H.D., Taylor W., Waterhouse P.M., and Wang M.-B. Agrobacterium-mediated transformation of Australian rice cultivars Jarrah and Amaroo using modified promoters and selectable markers. Aust. J. Plant Physiol. 27 (2000) 201-210
28. Siebert P.D., Chenchik A., Kellogg D.E., Lukyanov K.A., and Lukyanov S.A. An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res. 23 (1995) 1087-1088
29. Devic M., Albert S., Delseny M., and Roscoe T.J. Efficient PCR walking on plant genomic DNA. Plant Physiol. Biochem. 35 (1997) 331-339
30. Liu Y.G., Mitsukawa N., Oosumi T., and Whittier R.F. Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J. 8 (1995) 457-463
31. Zhu Q.-H., Hoque M.S., Dennis E.S., and Upadhyaya N.M. Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L.). BMC Plant Biol. 3 (2003) 6
32. Devereux J., Haeberli P., and Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12 (1984) 387-395
33. Krizkova L., and Hrouda M. Direct repeats of T-DNA integrated in tobacco chromosome: characterization of junction regions. Plant J. 16 (1998) 673-680
34. Stahl R., Horvath H., Van Fleet J., Voetz M., von Wettstein D., and Wolf N. T-DNA integration into the barley genome from single and double cassette vectors. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 2146-2151
35. van Attikum H., Bundock P., and Hooykaas P.J. Non-homologous end-joining proteins are required for Agrobacterium T-DNA integration. EMBO J. 20 (2001) 6550-6558
36. Friesner J., and Britt A.B. Ku80-and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration. Plant J. 34 (2003) 427-440
37. Gallego M.E., Bleuyard J.Y., Daoudal-Cotterell S., Jallut N., and White C.I. Ku80 plays a role in non-homologous recombination but is not required for T-DNA integration in Arabidopsis. Plant J. 35 (2003) 557-565
38. Li J., Vaidya M., White C., Vainstein A., Citovsky V., and Tzfira T. Involvement of KU80 in T-DNA integration in plant cells. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 19231-19236
39. Kumar S., and Fladung M. Transgene repeats in aspen: molecular characterisation suggests simultaneous integration of independent T-DNAs into receptive hotspots in the host genome. Mol. Gen. Genet. 264 (2000) 20-28
40. Afolabi A.S., Worland B., Snape J.W., and Vain P. A large-scale study of rice plants transformed with different T-DNAs provides new insights into locus composition and T-DNA linkage configurations. Theor. Appl. Genet. 109 (2004) 815-826
41. Preston C.R., Flores C.C., and Engels W.R. Differential usage of alternative pathways of double-strand break repair in Drosophila. Genetics 172 (2006) 1055-1068
42. Tinland B., Schoumacher F., Gloeckler V., Bravo-Angel A.M., and Hohn B. The Agrobacterium tumefaciens virulence D2 protein is responsible for precise integration of T-DNA into the plant genome. EMBO J. 14 (1995) 3585-3595