Summary
We established tobacco tumour cell lines from crown galls induced by Agrobacterium. Restriction fragments containing T-DNA/plant DNA junctions were cloned from one of the cell lines, which has a single copy of the T-DNA in a unique region of its genome. We also isolated a DNA fragment that contained the integration target site from nontransformed tobacco cells. Nucleotide sequence analyses showed that the right and left breakpoints of the T-DNA mapped ca. 7.3 kb internal to the right 25 by border and ca. 350 by internal to the left border respectively. When the nucleotide sequences around these breakpoints were compared with the sequence of the target, significant homology was seen between the region adjacent to the integration target site and both external regions of the T-DNA breakpoints. In addition, a short stretch of plant DNA in the vicinity of the integration site was deleted. This deletion seems to have been promoted by homologous recombination between short repeated sequences that were present on both sides of the deleted stretch. Minor rearrangements, which included base substitutions, insertions and deletions, also took place around the integration site in the plant DNA. These results, together with previously reported results showing that in some cases sequences homologous to those in T-DNA are present in plant DNA regions adjacent to left recombinational junctions, indicate that sequence homology between the incoming T-DNA and the plant chromosomal DNA has an important function in T-DNA integration. The homology may promote close association of both termini of a T-DNA molecule on a target sequence; then TDNA may in some cases be integrated by a mechanism at least in part analogous to homologous recombination.
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References
Albertini AM, Hofer M, Calos MP, Miller JH (1982) On the formation of spontaneous deletion: the importance of short sequence homologies in the generation of large deletions. Cell 29:319–328
Albright LM, Yanofsky MF, Leroux B, Ma D, Nester EW (1987) Processing of the T-DNA of Agrobacterium tumefaciens generates border nicks and linear, single-stranded T-DNA. J Bacteriol 169:1046–1055
Bakkeren G, Koukoliková-Nicola Z, Hohn B (1989) Recovery of Agrobacterium tumefaciens T-DNA molecules from whole plants early after transfer. Cell 57:847–857
Barker RF, Idler KB, Thompson DV, Kemp JD (1983) Nucleotide sequence of the T-DNA region from Agrobacterium tumefaciens octopine Ti plasmid pTil5955. Plant Mol Biol 2:335–350
Brutlag DL (1980) Molecular arrangement and evolution of heterochromatic DNA. Annu Rev Genet 14:121–144
Deroles SC, Gardner RC (1988) Analysis of the T-DNA structure in a large number of transgenic petunias generated by Agrobacterium-mediated transformation. Plant Mol Biol 11:365–377
Dixon LK, Hohn T (1984) Initiation of translation of the cauliflower mosaic virus genome from a polycistronic mRNA. EMBO J 3:2731–2736
Dürrenberger F, Crameri A, Hohn B, Koukolikova-Nicola Z (1989) Covalently bound VirD2 protein of Agrobacterium tumefaciens protects the T-DNA from exonucleolytic degradation. Proc Natl Acad Sci USA 86:9154–9158
Feinberg AP, Vogelstein B (1983) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6–13
Fraley RT, Horsch RB, Matzke A, Chilton M-D, Chilton WS, Sanders PR (1984) In vitro transformation of petunia cells by an improved method of co-cultivation with A. tumefaciens strains. Plant Mol Biol 3:371–378
Gheysen G, Van Montagu M, Zambryski P (1987) Integration of A. tumefaciens T-DNA involves rearrangements of target plant DNA sequences. Proc Natl Acad Sci USA 84:6169–6173
Gielen J, De Beuckeleer M, Seurinck J, Deboeck F, De Greve H, Lemmers M, Van Montagu M, Schell J (1984) The complete nucleotide sequence of the TL-DNA of the A. tumefaciens pTiAch5. EMBO J 3:835–846
Hamada H, Petrino MG, Kakunaga T (1982) A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79:6465–6469
Hepburn AG, Clarke LE, Blundy KS, White J (1983) Nopaline Ti-plasmid, pTiT37, T-DNA insertions into a flax genome. J Mol Appl Genet 2:221–224
Herrera-Estrella A, Chen Z, Van Montagu M, Wang K (1988) 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 7:4055–4062
Hohn B, Koukolíková-Nicola Z, Bakkeren G, Grimnsley N (1989) Agrobacterium-mediated gene transfer to monocots and dicots. Genome 31:987–993
Holsters M, Villarroel R, Gielen J, Seurinck J, De Greve H, Van Montagu M, Schell J (1983) An analysis of the boundaries of the octopine TL-DNA in tumors induced by Agrobacterium tumefaciens. Mol Gen Genet 190:35–41
Howard EA, Winsor BA, De Vos G, Zambryski P (1989) Activation of T-DNA transfer process in Agrobacterium results in the generation of a T-strand-protein complex: Tight association of VirD2 with the 5′ ends of T-strands. Proc Natl Acad Sci USA 86:4017–4021
Karn J, Matthes HWD, Gait MJ, Brenner S (1984) A new selective phage cloning vector, λ2001, with sites for XbaI, BamHI, HindIII, EcoRI, SstI and XhoI. Gene 32:217–224
Koncz C, Schell J (1986) The promoter of TL-DNA gene 5 controls the tissue-specific expression of chimeric genes carried by a novel type of Agrobacterium binary vector. Mol Gen Genet 204:383–396
Koukolíková-Nicola Z, Albright L, Hohn B (1987) The mechanism of T-DNA transfer from Agrobacterium tumefaciens to plant cell. In: Hohn T, Schell J (eds) Plant gene research, vol 4. Springer, Wien, pp 109–148
Kwok WW, Nester EW, Gordon MP (1985) Unusual plasmid organization in an octopine crown gall tumor. Nucleic Acids Res 13:459–471
Matsumoto S, Takebe I, Machida Y (1988) Escherichia coli lacZ gene as a biochemical and histochemical marker in plant cells. Gene 66:19–29
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
Nester EW, Gordon MP, Amasino RM, Yanofsky MF (1984) Crown gall: a molecular and physiological analysis. Annu Rev Plant Physiol 35:387–413
Ooms G, Bakker A, Molendijk L, Wullems GJ, Gordon MP, Nester EW, Schilperoort RA (1982) T-DNA organization in homogeneous and heterogeneous octopine-type crown gall tissues of Nicotiana tabacum. Cell 30:589–597
Paszkowski J, Baur M, Bogucki A, Potrykus I (1988) Gene targeting in plants. EMBO J 7:4021–4026
Peerbolte R, Leenhouts K, Hooykaas-van Slogteren GMS, Hoge JHC, Wullems GJ, Schilperoort RA (1986) Clones from a shooty tobacco crown gall tumor I: deletions, rearrangements and amplifications resulting in irregular T-DNA structures and organizations. Plant Mol Biol 7:265–284
Rich A, Nordheim A, Wang AH-J (1984) The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem 53:791–846
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, NY
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Simpson RB, O'Hara PJ, Kwok W, Montoya AL, Lichtenstein C, Gordon MP, Nester EW (1982) DNA from the A6/2 crown gall tumor contains scrambled Ti plasmid sequences near its junctions with the plant DNA. Cell 29:1005–1014
Spielmann A, Simpson RB (1986) T-DNA structure in transgenic tobacco plants with multiple independent integration sites. Mol Gen Genet 205:34–41
Stachel SE, Nester EW, Zambryski PC (1986) A plant cell factor induces Agrobacterium tumefaciens vir gene expression. Proc Natl Acad Sci USA 83:379–383
Van Haaren MJJ, Sedee NJA, Krul M, Schilperoort RA, Hooykaas PJJ (1988) Function of heterologous and pseudo border repeats in T region transfer via the octopine virulence system of Agrobacterium tumefaciens. Plant Mol Biol 11:773–781
Van Lijsebettens M, Inzé D, Schell J, Van Montagu M (1986) Transformed cell clones as a tool to study T-DNA integration mediated by Agrobacterium tumefaciens. J Mol Biol 188:129–145
Veluthambi K, Jayaswal RK, Gelvin SB (1987) Virulence genes A, G, and D mediate the double-stranded border cleavage of T-DNA from the Agrobacterium Ti plasmid. Proc Natl Acad Sci USA 84:1881–1885
Wang K, Herrera-Estrella L, Van Montagu M, Zambryski P (1984) Right 25 by terminus sequence of the nopaline T-DNA is essential for and determines direction of DNA transfer from Agrobacterium to the plant genome. Cell 38:455–462
Wang K, Stachel SE, Timmerman B, Van Montagu M, Zambryski PC (1987) Site-specific nick in the T-DNA border sequence as a result of Agrobacterium vir gene expression. Science 235:587–591
Ward ER, Barnes WM (1988) VirD2 protein of Agrobacterium tumefaciens very tightly linked to the 5′ end of T-strand DNA. Science 242:927–930
Winans SC, Kerstetter RA, Nester EW (1988) Transcriptional regulation of the virA and virG genes of Agrobacterium tumefaciens. J Bacteriol 170:4047–4054
Yadav NS, Vanderleyden J, Bennett DR, Barnes WM, Chilton M-D (1982) Short direct repeats flank the T-DNA on a nopaline Ti plasmid. Proc Natl Acad Sci USA 79:6322–6326
Yamamoto A, Iwahashi M, Yanofsky MF, Nester EW, Takebe I, Machida Y (1987) The promoter proximal region in the virD locus of Agrobacterium tumefaciens is necessary for the plantinducible circularization of T-DNA. Mol Gen genet 206:174–177
Yanofsky MF, Porter SG, Young C, Albright LM, Gordon MP, Nester EW (1986) The virD operon of Agrobacterium tumefaciens encodes a site-specific endonuclease. Cell 47:471–477
Young C, Nester EW (1988) Association of the VirD2 protein with the 5′ end of T strands in Agrobacterium tumefaciens. J Bacteriol 170:3367–3374
Zambryski P (1988) Basic processes underlying Agrobacterium-mediated DNA transfer to plant cells. Annu Rev Genet 22:1–30
Zambryski P, Depicker A, Kruger K, Goodman HM (1982) Tumor induction by Agrobacterium tumefaciens: analysis of the boundaries of T-DNA. J Mol Appl Genet 1:361–370
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Communicated by M. Sekiguchi
Shogo Matsumoto is on leave from Biochemical Research Institute, Nippon Menard Cosmetic Co., Ltd, Ogaki, Gifu-ken 503, Japan
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Matsumoto, S., Ito, Y., Hosoi, T. et al. Integration of Agrobacterium T-DNA into a tobacco chromosome: Possible involvement of DNA homology between T-DNA and plant DNA. Molec. Gen. Genet. 224, 309–316 (1990). https://doi.org/10.1007/BF00262423
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DOI: https://doi.org/10.1007/BF00262423