Recent patents on Agrobacterium-mediated gene and protein transfer, for research and biotechnology

Recent Patents on DNA and Gene Sequences

Volumn 2, Issue 2, 2008, Pages 69-81

  Lacroix, Benoît ^a   Kozlovsky, Stanislav V ^a   Citovsky, Vitaly ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

Agrobacterium; Agrobacterium tumefaciens; Agrobacterium mediated DNA transfer; Agrobacterium mediated gene transfer technology; DNA integration; Gene targeting; Genetic transformation; T DNA integration; VirB D4 T4SS; VirB VirD4 channel

Indexed keywords

ARABIDOPSIS PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; CRE RECOMBINASE; INTEGRASE;

BACTERIAL GENETICS; BACTERIAL VIRULENCE; CELL CONTACT; DNA INTEGRATION; DNA MODIFICATION; DNA TRANSFER; EUKARYOTIC CELL; FUNGUS; GENE TARGETING; GENE TECHNOLOGY; GENETIC TRANSFORMATION; HOST CELL; MACROMOLECULE; MEMBRANE CHANNEL; NONHUMAN; PATENT; PLANT BIOTECHNOLOGY; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN TRANSPORT; REVIEW; RHIZOBIUM RADIOBACTER; SEA URCHIN; SPECIES DIFFERENCE;

BIOTECHNOLOGY; PATENTS AS TOPIC; PLANTS, GENETICALLY MODIFIED; RHIZOBIUM; TRANSFORMATION, GENETIC;

AGROBACTERIUM; AGROBACTERIUM TUMEFACIENS; ANIMALIA; BACTERIA (MICROORGANISMS); ECHINOIDEA; EUKARYOTA; FUNGI;

EID: 55849099297     PISSN: 18722156     EISSN: None     Source Type: Journal    
DOI: 10.2174/187221508784534140     Document Type: Review

References (160)

1. Escobar MA, Dandekar AM. Agrobacterium tumefaciens as an agent of disease. Trends Plant Sci 2003; 8: 380-386.
2. Nilsson O, Olsson O. Getting to the root: the role of the Agrobacterium rhizogenes rol genes in the formation of hairy roots. Physiol Plant 1997; 100: 463-473.
3. Citovsky V, Kozlovsky SV, Lacroix B, et al. Biological systems of the host cell involved in Agrobacterium infection. Cell Microbiol 2007; 9: 9-20.
4. Gelvin SB. Agrobacterium and Plant genes involved in T-DNA Transfer and Integration. Annu Rev Plant Physiol Plant Mol Biol 2000; 51: 223-256.
5. Gelvin SB. Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol Mol Biol Rev 2003; 67: 16-37.
6. Tzfira T, Citovsky V. Partners-in-infection: host proteins involved in the transformation of plant cells by Agrobacterium. Trends Cell Biol 2002; 12: 121-129.
7. Zupan J, Muth TR, Draper O, Zambryski P. The transfer of DNA from Agrobacterium tumefaciens into plants: a feast of fundamental insights. Plant J 2000; 23: 11-28.
8. Newell CA. Plant transformation technology. Developments and applications. Mol Biotechnol 2000; 16: 53-65.
9. Lacroix B, Tzfira T, Vainstein A, Citovsky V. A case of promiscuity: Agrobacterium's endless hunt for new partners. Trends Genet 2006; 22: 29-37.
10. Bundock P, den Dulk-Ras A, Beijersbergen A, Hooykaas PJ. Trans-kingdom T-DNA transfer from Agrobacterium tumefaciens to Saccharomyces cerevisiae. EMBO J 1995; 14: 3206-3214.
11. Piers KL, Heath JD, Liang X, Stephens KM, Nester EW. Agrobacterium tumefaciens-mediated transformation of yeast. Proc Natl Acad Sci USA 1996; 93: 1613-1618.
12. de Groot MJ, Bundock P, Hooykaas PJ, Beijersbergen AG. Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol 1998; 16: 839-842.
13. Michielse CB, Hooykaas PJ, van den Hondel CA, Ram AF. Agrobacterium-mediated transformation as a tool for functional genomics in fungi. Curr Genet 2005; 48: 1-17.
14. Bulgakov VP, Kiselev KV, Yakovlev KV, Zhuravlev YN, Gontcharov AA, Odintsova NA. Agrobacterium-mediated transformation of sea urchin embryos. Biotechnol J 2006; 1: 454-461.
15. Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V. Genetic transformation of HeLa cells by Agrobacterium. Proc Natl Acad Sci USA 2001; 98: 1871-1876.
16. Nottenburg C, Rodriguez CR. Agrobacterium mediated gene transfer: A lawyer's perspective. In: Tzfira T, Citovsky V, eds. Agrobacterium: From Biology to Biotechnology: Springer 2008; 699-735.
17. Roa-Rodriguez C, Nottenburg C. Agrobacterium-mediated transformation of plants. Cambia technology landscape paper 2003 http://www.bios.net/Agrobacterium
18. Chilton MD, Saiki RK, Yadav N, Gordon MP, Quetier F. T-DNA from Agrobacterium Ti plasmid is in the nuclear DNA fraction of crown gall tumor cells. Proc Natl Acad Sci USA 1980; 77: 4060-4064.
19. Peralta EG, Ream LW. T-DNA border sequences required for crown gall tumorigenesis. Proc Natl Acad Sci USA 1985; 82: 5112-5116.
20. Klee HJ, White FF, Iyer VN, Gordon MP, Nester EW. Mutational analysis of the virulence region of an Agrobacterium tumefaciens Ti plasmid. J Bacteriol 1983; 153: 878-883.
21. Stachel SE, Nester EW. The genetic and transcriptional organization of the vir region of the A6 Ti plasmid of Agrobacterium tumefaciens. EMBO J 1986; 5: 1445-1454.
22. An G, Watson BD, Chiang CC. Transformation of tobacco, tomato, potato, and Arabidopsis thaliana using a binary Ti vector system. Plant Physiol 1986; 81: 301-305.
23. Lee LY, Gelvin SB. T-DNA binary vectors and systems. Plant Physiol 2008; 146: 325-332.
24. Lee YW, Jin S, Sim WS, Nester EW. Genetic evidence for direct sensing of phenolic compounds by the VirA protein of Agrobacterium tumefaciens. Proc Natl Acad Sci USA 1995; 92: 12245-12249.
25. Lee YW, Jin S, Sim WS, Nester EW. The sensing of plant signal molecules by Agrobacterium: genetic evidence for direct recognition of phenolic inducers by the VirA protein. Gene 1996; 179: 83-88.
26. McLean BG, Greene EA, Zambryski PC. Mutants of Agrobacterium VirA that activate vir gene expression in the absence of the inducer acetosyringone. J Biol Chem 1994; 269: 2645-2651.
27. Stachel SE, Nester EW, Zambryski PC. A plant cell factor induces Agrobacterium tumefaciens vir gene expression. Proc Natl Acad Sci USA 1986; 83: 379-383.
28. Bolton GW, Nester EW, Gordon MP. Plant phenolic compounds induce expression of the Agrobacterium tumefaciens loci needed for virulence. Science 1986; 232: 983-985.
29. Cangelosi GA, Ankenbauer RG, Nester EW. Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proc Natl Acad Sci USA 1990; 87: 6708-6712.
30. Peng WT, Lee YW, Nester EW. The phenolic recognition profiles of the Agrobacterium tumefaciens VirA protein are broadened by a high level of the sugar binding protein ChvE. J Bacteriol 1998; 180: 5632-5638.
31. Stachel SE, Zambryski PC. virA and virG control the plant-induced activation of the T-DNA transfer process of A. tumefaciens. Cell 1986; 46: 325-333.
32. Scheiffele P, Pansegrau W, Lanka E. Initiation of Agrobacterium tumefaciens T-DNA processing. Purified proteins VirD1 and VirD2 catalyze site- and strand-specific cleavage of superhelical T-border DNA in vitro. J Biol Chem 1995; 270: 1269-1276.
33. Durrenberger F, Crameri A, Hohn B, Koukolikova-Nicola Z. Covalently bound VirD2 protein of Agrobacterium tumefaciens protects the T-DNA from exonucleolytic degradation. Proc Natl Acad Sci USA 1989; 86: 9154-9158.
34. Pansegrau W, Schoumacher F, Hohn B, Lanka E. Site-specific cleavage and joining of single-stranded DNA by VirD2 protein of Agrobacterium tumefaciens Ti plasmids: analogy to bacterial conjugation. Proc Natl Acad Sci USA 1993; 90: 11538-11542.
35. Young C, Nester EW. Association of the virD2 protein with the 5′ end of T strands in Agrobacterium tumefaciens. J Bacteriol 1988; 170: 3367-3374.
36. Danhorn T, Fuqua C. Biofilm formation by plant-associated bacteria. Annu Rev Microbiol 2007; 61: 401-422.
37. Rodriguez-Navarro DN, Dardanelli MS, Ruiz-Sainz JE. Attachment of bacteria to the roots of higher plants. FEMS Microbiol Lett 2007; 272: 127-136.
38. Wagner VT, Matthysse AG. Involvement of a vitronectin-like protein in attachment of Agrobacterium tumefaciens to carrot suspension culture cells. J Bacteriol 1992; 174: 5999-6003.
39. Nam J, Mysore KS, Zheng C, Knue MK, Matthysse AG, Gelvin SB. Identification of T-DNA tagged Arabidopsis mutants that are resistant to transformation by Agrobacterium. Mol Gen Genet 1999; 261: 429-438.
40. Gaspar YM, Nam J, Schultz CJ, et al. Characterization of the Arabidopsis lysine-rich arabinogalactan-protein AtAGP17 mutant (rat1) that results in a decreased efficiency of Agrobacterium transformation. Plant Physiol 2004; 135: 2162-2171.
41. Hwang HH, Gelvin SB. Plant proteins that interact with VirB2, the Agrobacterium tumefaciens pilin protein, mediate plant transformation. Plant Cell 2004; 16: 3148-3167.
42. Matthysse AG. Role of bacterial cellulose fibrils in Agrobacterium tumefaciens infection. J Bacteriol 1983; 154: 906-915.
43. Christie PJ. Type IV secretion: the Agrobacterium VirB/D4 and related conjugation systems. Biochim Biophy Acta 2004; 1694: 219-234.
44. Kado CI. The role of the T-pilus in horizontal gene transfer and tumorigenesis. Curr Opin Microbiol 2000; 3: 643-648.
45. Citovsky V, Zupan J, Warnick D, Zambryski P. Nuclear localization of Agrobacterium VirE2 protein in plant cells. Science 1992; 256: 1802-1805.
46. Gelvin SB. Agrobacterium VirE2 proteins can form a complex with T strands in the plant cytoplasm. J Bacteriol 1998; 180: 4300-4302.
47. Vergunst AC, Schrammeijer B, den Dulk-Ras A, et al. VirB/ D4-dependent protein translocation from Agrobacterium into plant cells. Science 2000; 290: 979-982.
48. Schrammeijer B, den Dulk-Ras A, Vergunst AC, Jurado Jacome E, Hooykaas PJ. Analysis of Vir protein translocation from Agrobacterium tumefaciens using Saccharomyces cerevisiae as a model: evidence for transport of a novel effector protein VirE3. Nucleic Acids Res 2003; 31: 860-868.
49. Lacroix B, Vaidya M, Tzfira T, Citovsky V. The VirE3 protein of Agrobacterium mimics a host cell function required for plant genetic transformation. EMBO J 2005; 24: 428-437.
50. Vergunst AC, van Lier MC, den Dulk-Ras A, Stuve TA, Ouwehand A, Hooykaas PJ. Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium. Proc Natl Acad Sci USA 2005; 102: 832-837.
51. Grange W, Duckely M, Husale S, Jacob S, Engel A, Hegner M. VirE2: a unique ssDNA-compacting molecular machine. PLoS Biol 2008; 6: e44.
52. Christie PJ, Ward JE, Winans SC, Nester EW. The Agrobacterium tumefaciens virE2 gene product is a single-stranded-DNA-binding protein that associates with T-DNA. J Bacteriol 1988; 170: 2659-2667.
53. Citovsky V, Wong ML, Zambryski P. Cooperative interaction of Agrobacterium VirE2 protein with single-stranded DNA: implications for the T-DNA transfer process. Proc Natl Acad Sci USA 1989; 86: 1193-1197.
54. Das A. Agrobacterium tumefaciens virE operon encodes a singles-tranded DNA-binding protein. Proc Natl Acad Sci USA 1988; 85: 2909-2913.
55. Citovsky V, De Vos G, Zambryski P. Single-Stranded DNA Binding Protein Encoded by the virE Locus of Agrobacterium tumefaciens. Science 1988; 240: 501-504.
56. Citovsky V, Guralnick B, Simon MN, Wall JS. The molecular structure of Agrobacterium VirE2-single stranded DNA complexes involved in nuclear import. J Mol Biol 1997; 271: 718-727.
57. Abu-Arish A, Frenkiel-Krispin D, Fricke T, et al. Three-dimensional reconstruction of Agrobacterium VirE2 protein with single-stranded DNA. J Biol Chem 2004; 279: 25359-25363.
58. Guralnick B, Thomsen G, Citovsky V. Transport of DNA into the nuclei of Xenopus oocytes by a modified VirE2 protein of Agrobacterium. Plant Cell 1996; 8: 363-373.
59. Tzfira T, Citovsky V. Comparison between nuclear import of nopaline- and octopine-specific VirE2 protein of Agrobacterium in plant and animal cells. Mol Plant Pathol 2001; 2: 171-176.
60. Tzfira T, Vaidya M, Citovsky V. VIP1, an Arabidopsis protein that interacts with Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. EMBO J 2001; 20: 3596-3607.
61. Sen P, Pazour GJ, Anderson D, Das A. Cooperative binding of Agrobacterium tumefaciens VirE2 protein to single-stranded DNA. J Bacteriol 1989; 171: 2573-2580.
62. Ballas N, Citovsky V. Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Agrobacterium VirD2 protein. Proc Natl Aca Sci USA 1997; 94: 10723-10728.
63. Tzfira T, Vaidya M, Citovsky V. Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. Proc Natl Acad Sci USA 2002; 99: 10435-10440.
64. Lacroix B, Li J, Tzfira T, Citovsky V. Will you let me use your nucleus? How Agrobacterium gets its T-DNA expressed in the host plant cell. Can J Physiol Pharm 2006; 84: 333-345.
65. Djamei A, Pitzschke A, Nakagami H, Rajh I, Hirt H. Trojan horse strategy in Agrobacterium transformation: abusing MAPK defense signaling. Science 2007; 318: 453-456.
66. Ziemienowicz A, Merkle T, Schoumacher F, Hohn B, Rossi L. Import of Agrobacterium T-DNA into plant nuclei: two distinct functions of VirD2 and VirE2 proteins. Plant Cell 2001; 13: 369-383.
67. Tzfira T. On tracks and locomotives: the long route of DNA to the nucleus. Trends Microbiol 2006; 14: 61-63.
68. Hodges LD, Cuperus J, Ream W. Agrobacterium rhizogenes GALLS protein substitutes for Agrobacterium tumefaciens single-stranded DNA-binding protein VirE2. J Bacteriol 2004; 186: 3065-3077.
69. Hodges LD, Vergunst AC, Neal-McKinney J, et al. Agrobacterium rhizogenes GALLS protein contains domains for ATP binding, nuclear localization, and type IV secretion. J Bacteriol 2006; 188: 8222-8230.
70. Li J, Krichevsky A, Vaidya M, Tzfira T, Citovsky V. Uncoupling of the functions of the Arabidopsis VIP1 protein in transient and stable plant genetic transformation by Agrobacterium. Proc Natl Acad Sci USA 2005; 102: 5733-5738.
71. Loyter A, Rosenbluh J, Zakai N, et al. The plant VirE2 interacting protein 1. a molecular link between the Agrobacterium T-complex and the host cell chromatin? Plant Physiol 2005; 138: 1318-1321.
72. Schrammeijer B, Risseeuw E, Pansegrau W, et al. Interaction of the virulence protein VirF of Agrobacterium tumefaciens with plant homologs of the yeast Skp1 protein. Curr Biol 2001; 11: 258-262.
73. Tzfira T, Vaidya M, Citovsky V. Involvement of targeted proteolysis in plant genetic transformation by Agrobacterium. Nature 2004; 431: 87-92.
74. Tzfira T, Li J, Lacroix B, Citovsky V. Agrobacterium T-DNA integration: molecules and models. Trends Genet 2004; 20: 375-383.
75. Tinland B, Hohn B. Recombination between prokaryotic and eukaryotic DNA: integration of Agrobacterium tumefaciens T-DNA into the plant genome. Genet Eng 1995; 17: 209-229.
76. De Neve M, De Buck S, Jacobs A, Van Montagu M, 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 1997; 11: 15-29.
77. De Buck S, Jacobs A, Van Montagu M, 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 1999; 20: 295-304.
78. Tzfira T, Frankman LR, Vaidya M, Citovsky V. Site-specific integration of Agrobacterium tumefaciens T-DNA via double-stranded intermediates. Plant Physiol 2003; 133: 1011-1023.
79. Chilton MD, 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 2003; 133: 956-965.
80. Anand A, Krichevsky A, Schornack S, et al. Arabidopsis VIRE2 INTERACTING PROTEIN2 is required for Agrobacterium T-DNA integration in plants. Plant Cell 2007; 19: 1695-1708.
81. Gelvin SB, Kim SI. Effect of chromatin upon Agrobacterium T-DNA integration and transgene expression. Biochim Biophys Acta 2007; 1769: 410-421.
82. Gelvin SB. Agrobacterium virulence gene induction. Methods Mol Biol 2006; 343: 77-84.
83. Jin SG, Komari T, Gordon MP, Nester EW. Genes responsible for the supervirulence phenotype of Agrobacterium tumefaciens A281. J Bacteriol 1987; 169: 4417-4425.
84. Wang K, Herrera-Estrella A, Van Montagu M. Overexpression of virD1 and virD2 genes in Agrobacterium tumefaciens enhances T-complex formation and plant transformation. J Bacteriol 1990; 172: 4432-4440.
85. Tang W. Additional virulence genes and sonication enhance Agrobacterium tumefaciens-mediated loblolly pine transformation. Plant Cell Rep 2003; 21: 555-562.
86. Chateau S, Sangwan RS, Sangwan-Norreel BS. Competence of Arabidopsis thaliana genotypes and mutants for Agrobacterium tumefaciens-mediated gene transfer: role of phytohormones. J Exp Bot 2000; 51: 1961-1968.
87. Sandal I, Saini U, Lacroix B, Bhattacharya A, Ahuja PS, Citovsky V. Agrobacterium-mediated genetic transformation of tea leaf explants: effects of counteracting bactericidity of leaf polyphenols without loss of bacterial virulence. Plant Cell Rep 2007; 26: 169-176.
88. Gelvin SB. Improving plant genetic engineering by manipulating the host. Trends Biotech 2003; 21: 95-98.
89. Reavy, B., Taliansky, M.E., Kim, S.H., Vartapetian, A.B., Chichkova, N.V., Bagirova, S.: WO07132193 (2007).
90. Chichkova NV, Kim SH, Titova ES, et al. A plant caspase-like protease activated during the hypersensitive response. Plant Cell 2004; 16: 157-171.
91. Bonneau L, Ge Y, Drury GE, Gallois P. What happened to plant caspases? J Exp Bot 2008; 59:491-499.
92. Reavy B, Bagirova S, Chichkova NV, et al. Caspase-resistant VirD2 protein provides enhanced gene delivery and expression in plants. Plant Cell Rep 2007; 26: 1215-1219.
93. Eomo, H., Minamizawa, K., Nonaka, S., Sugawara, M.: JP05312345 (2005).
94. Mur LA, Kenton P, Lloyd AJ, Ougham H, Prats E. The hypersensitive response; the centenary is upon us but how much do we know? J Exp Bot 2008; 59:501-520.
95. Greenberg JT, Yao N. The role and regulation of programmed cell death in plant-pathogen interactions. Cell Micro 2004; 6: 201-211.
96. Veena, JH, Doerge RW, Gelvin SB. Transfer of T-DNA and Vir proteins to plant cells by Agrobacterium tumefaciens induces expression of host genes involved in mediating transformation and suppresses host defense gene expression. Plant J 2003; 35: 219-236.
97. Ditt RF, Nester E, Comai L. The plant cell defense and Agrobacterium tumefaciens. FEMS Microbiol Lett 2005; 247: 207-213.
98. Ditt RF, Kerr KF, de Figueiredo P, Delrow J, Comai L, Nester EW. The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens. Mol Plant Microbe Interact 2006; 19: 665-681.
99. Dunoyer P, Himber C, Voinnet O. Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens infections. Nat Genet 2006; 38: 258-263.
100. Yuan ZC, Edlind MP, Liu P, et al. The plant signal salicylic acid shuts down expression of the vir regulon and activates quormone-quenching genes in Agrobacterium. Proc Natl Acad Sci USA 2007; 104:11790-11795.
101. Broekaert WF, Delaure SL, De Bolle MF, Cammue BP. The role of ethylene in host-pathogen interactions. Annu Rev Phytopathol 2006; 44: 393-416.
102. Nonaka S, Yuhashi KI, Takada K, Sugaware M, Minamisawa K, Ezura H. Ethylene production in plants during transformation suppresses vir gene expression in Agrobacterium tumefaciens. New Phytol 2008; 178:647-56.
103. Glick BR. Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. FEMS Microbiol Lett 2005; 251: 1-7.
104. Nonaka S, Sugawara M, Minamisawa K, Yuhashi KI, Ezura H. 1-aminocyclopropane-1-carboxylate deaminase-producing Agrobacterium tumefaciens has higher ability for gene transfer into plant cells. Appl Environ Microbiol 2008; 74: 2526-28.
105. Tzfira, T., Citovsky, V.: WO04035731 (2004).
106. Frame, B.R., Wang, K., Mysore, K.S., Gelvin, S.B. US2007 7279336 (2007).
107. Mysore, K.S., Gelvin, S.B.: US20077276374 (2007).
108. Crane YM, Gelvin SB. RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation. Proc Natl Acad Sci USA 2007; 104: 15156-15161.
109. Mysore KS, Nam J, Gelvin SB. An Arabidopsis histone H2A mutant is deficient in Agrobacterium T-DNA integration. Proc Natl Acad Sci USA 2000; 97: 948-953.
110. Yi H, Sardesai N, Fujinuma T, Chan CW, Veena, Gelvin SB. Constitutive expression exposes functional redundancy between the Arabidopsis histone H2A gene HTA1 and other H2A gene family members. Plant Cell 2006; 18: 1575-1589.
111. Anand A, Vaghchhipawala Z, Ryu CM, et al. Identification and characterization of plant genes involved in Agrobacterium-mediated plant transformation by virus-induced gene silencing. Mol Plant Microbe Interact 2007; 20: 41-52.
112. Britt AB, May GD. Re-engineering plant gene targeting. Trends Plant Sci 2003; 8: 90-95.
113. Hanin M, Volrath S, Bogucki A, Briker M, Ward E, Paszkowski J. Gene targeting in Arabidopsis. Plant J 2001; 28: 671-677.
114. Hanin M, Paszkowski J. Plant genome modification by homologous recombination. Curr Opin Plant Biol 2003; 6: 157-162.
115. Alonso JM, Stepanova AN, Leisse TJ, et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 2003; 301: 653-657.
116. Feldmann KA. T-DNA insertion mutagenesis in Arabidopsis: mutational spectrum. Plant J 1991; 1: 71-82.
117. Brunaud V, Balzergue S, Dubreucq B, et al. T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep 2002; 3: 1152-1157.
118. Szabados L, Kovacs I, Oberschall A, et al. Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome. Plant J 2002; 32: 233-242.
119. Chen S, Jin W, Wang M, et al. Distribution and characterization of over 1000 T-DNA tags in rice genome. Plant J 2003; 36: 105-113.
120. Sallaud C, Gay C, Larmande P, et al. High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics. Plant J 2004; 39: 450-464.
121. Choi J, Park J, Jeon J, et al. Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae. Mol Microbiol 2007; 66: 371-382.
122. Kim SI, Veena V, Gelvin SB. Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions. Plant J 2007; 51: 779-791.
123. Dominguez A, Fagoaga C, Navarro L, Moreno P, Pena L. Regeneration of transgenic citrus plants under non selective conditions results in high-frequency recovery of plants with silenced transgenes. Mol Genet Genomics 2002; 267: 544-556.
124. Francis KE, Spiker S. Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations. Plant J 2005; 41: 464-477.
125. Shaked H, Melamed-Bessudo C, Levy AA. High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc Natl Acad Sci USA 2005; 102: 12265-12269.
126. Scott CT. The zinc finger nuclease monopoly. Nat Biotechnol 2005; 23: 915-918.
127. Mandell JG, Barbas CF 3rd. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res 2006; 34: W516-23.
128. Miller JC, Holmes MC, Wang J, et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 2007; 25: 778-785.
129. Wright DA, Townsend JA, Winfrey RJ Jr, et al. High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J 2005; 44: 693-705.
130. Groth AC, Calos MP. Phage integrases: biology and applications. J Mol Biol 2004; 335: 667-678.
131. Landy A. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu Rev Biochem 1989; 58: 913-949.
132. Groth AC, Olivares EC, Thyagarajan B, Calos MP. A phage integrase directs efficient site-specific integration in human cells. Proc Natl Acad Sci USA 2000; 97: 5995-6000.
133. Chalberg TW, Portlock JL, Olivares EC, et al. Integration specificity of phage phiC31 integrase in the human genome. J Mol Biol 2006; 357: 28-48.
134. Ow, D.W.: US20056936747 (2005).
135. Lutz KA, Corneille S, Azhagiri AK, Svab Z, Maliga P. A novel approach to plastid transformation utilizes the phiC31 phage integrase. Plant J 2004; 37: 906-913.
136. Hooykaas, P.J., Van Attikum, H., Bundock, P.: WO02052026 (2002).
137. Vergunst AC, Jansen LE, Hooykaas PJ. Site-specific integration of Agrobacterium T-DNA in Arabidopsis thaliana mediated by Cre recombinase. Nucleic Acids Res 1998; 26: 2729-2734.
138. Vergunst AC, Hooykaas PJ. Cre/lox-mediated site-specific integration of Agrobacterium T-DNA in Arabidopsis thaliana by transient expression of cre. Plant Mol Biol 1998; 38: 393-406.
139. Louwerse JD, van Lier MC, van der Steen DM, de Vlaam CM, Hooykaas PJ, Vergunst AC. Stable recombinase-mediated cassette exchange in arabidopsis using Agrobacterium tumefaciens. Plant Physiol 2007; 145: 1282-1293.
140. van Attikum H, Bundock P, Hooykaas PJ. Non-homologous endjoining proteins are required for Agrobacterium T-DNA integration. EMBO J 2001; 20: 6550-6558.
141. van Attikum H, Hooykaas PJ. Genetic requirements for the targeted integration of Agrobacterium T-DNA in Saccharomyces cerevisiae. Nucleic Acids Res 2003; 31: 826-832.
142. Tan TL, Kanaar R, Wyman C. Rad54, a Jack of all trades in homologous recombination. DNA Repair 2003; 2: 787-794.
143. Mahajan, P.B., Shi, J.: US20067034117 (2006).
144. Mahajan, P.B.: US20067060480 (2006).
145. Sung P, Krejci L, Van Komen S, Sehorn MG. Rad51 recombinase and recombination mediators. J Biol Chem 2003; 278: 42729-42732.
146. Sonti RV, Chiurazzi M, Wong D, et al. Arabidopsis mutants deficient in T-DNA integration. Proc Natl Acad Sci USA 1995; 92: 11786-11790.
147. Usui T, Ohta T, Oshiumi H, Tomizawa J, Ogawa H, Ogawa T. Complex formation and functional versatility of Mre11 of budding yeast in recombination. Cell 1998; 95: 705-716.
148. Otten L, De Greve H, Leemans J, Hain R, Hooykaas PJ, Schell FM. Restoration of virulence of vir region mutants of A. tumefaciens strain B6S3 by coinfection with normal and mutants Agrobacterium strains. Mol Gen Genet 1984; 195: 159-163.
149. Christie PJ, Atmakuri K, Krishnamoorthy V, Jakubowski S, Cascales E. Biogenesis, architecture, and function of bacterial type IV secretion systems. Annu Rev Microbiol 2005; 59: 451-485.
150. Gordon-Kamm, B., Lowe, K.S., Bailey, M.A., Gelvin, S.B., Bhattacharjee, S., Tao, Y.: US20046800791 (2004).
151. Hooykaas, P.J., Vergunst, A.C., Schrammeijer, B.: WO01089283 (2001).
152. Dumas, F., Van Gelder, P., Duckely, M., Hohn, B., Pelczar, P.: WO01064923 (2001).
153. Dumas F, Duckely M, Pelczar P, Van Gelder P, Hohn B. An Agrobacterium VirE2 channel for transferred-DNA transport into plant cells. Proc Natl Acad Sci USA 2001; 98: 485-490.
154. Machida, C., Nakamura, K.: WO07138712 (2007).
155. Tinland B, Fournier P, Heckel T, Otten L. Expression of a chimaeric heat-shock-inducible Agrobacterium 6b oncogene in Nicotiana rustica. Plant Mol Biol 1992; 18: 921-930.
156. Wabiko H, Minemura M. Exogenous phytohormone-independent growth and regeneration of tobacco plants transgenic for the 6b gene of Agrobacterium tumefaciens AKE10. Plant Physiol 1996; 112: 939-951.
157. Clement B, Pollmann S, Weiler E, Urbanczyk-Wochniak E, Otten L. The Agrobacterium vitis T-6b oncoprotein induces auxin-independent cell expansion in tobacco. Plant J 2006; 45: 1017-1027.
158. Terakura S, Kitakura S, Ishikawa M, et al. Oncogene 6b from Agrobacterium tumefaciens induces abaxial cell division at late stages of leaf development and modifies vascular development in petioles. Plant Cell Physiol 2006; 47: 664-672.
159. Terakura S, Ueno Y, Tagami H, et al. An oncoprotein from the plant pathogen Agrobacterium has histone chaperone-like activity. Plant Cell 2007; 19: 2855-2865.
160. Tzfira T, Citovsky V. Agrobacterium-mediated genetic transformation of plants: biology and biotechnology. Curr Opinion Biotechnol 2006; 17: 147-154.