Improved gene targeting and nucleic acid carrier molecule, in particular for use in plants

Verbessertes Gen-Targeting und Nucleinsäureträgermoleküle, insbesondere zur Verwendung bei Pflanzen

Ciblage génique amélioré et molécule porteuse d'acide nucléique, en particulier pour utilisation dans des plantes

Abstract

The present invention relates to a nucleic acid carrier molecule, comprising the general formula M-S 1 -L-W-S 2 , wherein M is a first polypeptide specifically binding to a donor nucleic acid sequence to be transferred into an organelle of a cell, W is a second polypeptide specifically binding to a target nucleic acid sequence, wherein said target nucleic acid sequence is located in an organelle of a cell, L is missing or is linking group allowing M and W flexibility and semi-independence, and S 1 and S 2 independently of each other are missing or are a signal peptide sequence, and can be fused to M and W proteins either N-or C-terminally, wherein said donor nucleic acid sequence is brought into close proximity with said target nucleic acid sequence when both nucleic acid sequences are bound to said carrier molecule. The present invention furthermore relates to methods for recombinantly transforming a nucleic acid into an organelle in a cell, preferably a plant cell, employing said nucleic acid carrier molecule.

Claims

Description

Topics

Download Full PDF Version (Non-Commercial Use)

Patent Citations (6)

    Publication numberPublication dateAssigneeTitle
    US-2011145940-A1June 16, 2011Voytas Daniel F, Adam Bogdanove, Feng Zhang, Michelle Christian, Tomas Cermak, Clarice Lauer Schmidt, Erin Doyle, Li WangTal effector-mediated dna modification
    WO-03080809-A2October 02, 2003Sangamo Biosciences, Inc.Procedes et compositions permettant d'utiliser des endonucleases a doigts de zinc pour ameliorer la recombinaison homologue
    WO-2009042186-A2April 02, 2009Sangamo Biosciences, Inc., The Regents Of The University Of CaliforniaGenomic editing in zebrafish using zinc finger nucleases
    WO-2010079430-A1July 15, 2010Ulla Bonas, Jens Boch, Sebastian Schornack, Thomas LahayeDomaines modulaires de liaison à l'adn et procédés d'utilisation
    WO-2011072246-A2June 16, 2011Regents Of The University Of Minnesota, Iowa State University Research Foundation, Inc.Tal effector-mediated dna modification
    WO-2012168304-A1December 13, 2012Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)Protéine ayant une activité nucléase, protéines de fusion et leurs utilisations

NO-Patent Citations (59)

    Title
    ALONSO, J.M. ET AL.: "Genome-wide insertional mutagenesis of Arabidopsis thaliana", SCIENCE, vol. 301, 2003, pages 653 - 657, XP002300984, DOI: doi:10.1126/science.1086391
    BASS, B. L.: "RNA editing by adenosine deaminases that act on RNA", ANNUAL REVIEW OF BIOCHEMISTRY, vol. 71, no. 1, 2002, pages 817 - 846, XP002336892
    BITINAITE, J.; WAH, D.A.; AGGARWAL, A.K.; SCHILDKRAUT, I.: "Fokl dimerization is required for DNA cleavage", PROC NATL ACAD SCI U S A, vol. 95, 1998, pages 10570 - 10575, XP002212149, DOI: doi:10.1073/pnas.95.18.10570
    BOCH, J. ET AL.: "Breaking the code of DNA binding specificity of TAL-type III effectors", SCIENCE, vol. 326, 2009, pages 1509 - 1512
    BRAVO-ANGEL, A.M.; GLOECKLER, V.; HOHN, B.; TINLAND, B: "Bacterial conjugation protein MobA mediates integration of complex DNA structures into plant cells", J BACTERIOL, vol. 181, 1999, pages 5758 - 5765, XP002176994
    BRAVO-ANGEL, A.M.; HOHN, B.; TINLAND, B.: "The omega sequence ofVirD2 is important but not essential for efficient transfer of T-DNA by Agrobacterium tumefaciens", MOL PLANT MICROBE INTERACT, vol. 11, 1998, pages 57 - 63, XP002448303, DOI: doi:10.1094/MPMI.1998.11.1.57
    BUTTNER, D.: "Protein Export According to Schedule: Architecture, Assembly, and Regulation of Type III Secretion Systems from Plant- and Animal-Pathogenic Bacteria", MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, vol. 76, 2012, pages 262 - 310
    CAI, C. ET AL.: "Targeted transgene integration in plant cells using designed zinc finger nucleases", PLANT MOLECULAR BIOLOGY, vol. 69, 2009, pages 699 - 709, XP019686526
    CERMAK, T.; DOYLE, E.L.; CHRISTIAN, M.; WANG, L.; ZHANG, Y.; SCHMIDT, C.; BALLER, J.A.; SO- MIA, N.V.; BOGDANOVE, A.J.; VOYTAS, D.: "Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting", NUCLEIC ACIDS RES, vol. 39, 2011, pages 82, XP055130093, DOI: doi:10.1093/nar/gkr218
    CHARLES Q CAI ET AL: "Targeted transgene integration in plant cells using designed zinc finger nucleases", PLANT MOLECULAR BIOLOGY, KLUWER ACADEMIC PUBLISHERS, DORDRECHT, NL, vol. 69, no. 6, 27 December 2008 (2008-12-27), pages 699 - 709, XP019686526, ISSN: 1573-5028
    CITOVSKY, V.; ZALTSMAN, A.; KOZLOVSKY, S.V.; GAFNI, Y.; KRICHEVSKY, A.: "Pro- teasomal degradation in plant-pathogen interactions", SEMIN CELL DEV BIOL., 2009
    CONG, L. ET AL.: "Multiplex Genome Engineering Using CRISPR/Cas Systems", SCIENCE, vol. 339, 2013, pages 819 - 823, XP055153567, DOI: doi:10.1126/science.1231143
    DA CUNHA, L.; SREEREKHA, M.V.; MACKEY, D: "Defense suppression by virulence effectors of bacterial phytopathogens", CURR OPIN PLANT BIOL, vol. 10, 2007, pages 349 - 357, XP022182410, DOI: doi:10.1016/j.pbi.2007.04.018
    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 U S A, vol. 86, 1989, pages 9154 - 9158, XP001084199, DOI: doi:10.1073/pnas.86.23.9154
    F. FAUSER ET AL: "In planta gene targeting", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, vol. 109, no. 19, 8 May 2012 (2012-05-08), pages 7535 - 7540, XP055031401, ISSN: 0027-8424, DOI: 10.1073/pnas.1202191109
    FAUSER, F.; ROTH, N.; PACHER, M.; ILG, G.; SANCHEZ-FERNANDEZ, R.; BIESGEN, C.; PUCHTA, H.: "In planta gene targeting", PROC NATL ACAD SCI U S A, vol. 109, 2012, pages 7535 - 7540, XP055031401, DOI: doi:10.1073/pnas.1202191109
    GELVIN, S.B.: "Agrobacterium in the genomics age", PLANT PHYSIOL, vol. 150, 2009, pages 1665 - 1676, XP055016897, DOI: doi:10.1104/pp.109.139873
    HAO CHEN ET AL: "Promise and issues of genetically modified crops", CURRENT OPINION IN PLANT BIOLOGY, vol. 16, no. 2, 1 May 2013 (2013-05-01), pages 255 - 260, XP055070912, ISSN: 1369-5266, DOI: 10.1016/j.pbi.2013.03.007
    INDIO V; MARTELLI PL; SAVOJARDO C; FARISELLI P; CASADIO R: "The prediction of organelle- targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields", BIOINFORMATICS, vol. 29, no. 8, 15 April 2013 (2013-04-15), pages 981 - 8, Retrieved from the Internet
    IYER, L. M.; D. ZHANG ET AL.: "Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems", NUCLEIC ACIDS RES, vol. 39, no. 22, 2011, pages 9473 - 97
    JARCHOW, E.; GRIMSLEY, N.H.; HOHN, B.: "virF, the host-range-determining virulence gene of Agrobacterium tumefaciens, affects T-DNA transfer to Zea mays", PROC NATL ACAD SCI US A, vol. 88, 1991, pages 10426 - 10430
    JAYASWAL, R.K.; VELUTHAMBI, K.; GELVIN, S.B.; SLIGHTOM, J.L.: "Double-stranded cleavage of T-DNA and generation of single-stranded T-DNA molecules in Escherichia coli by a virD-encoded border-specific endonuclease from Agrobacterium tumefaciens", J BACTERIOL, vol. 169, 1987, pages 5035 - 5045
    JINEK, M.; CHYLINSKI, K.; FONFARA, I.; HAUER, M.; DOUDNA, J.A.; CHARPENTIER, E.: "A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity", SCIENCE, vol. 337, 2012, pages 816 - 821, XP055067747, DOI: doi:10.1126/science.1225829
    KAY, S.; BONAS, U.: "How Xanthomonas type III effectors manipulate the host plant", CURR OPIN MICROBIOL, vol. 12, 2009, pages 37 - 43, XP026194634, DOI: doi:10.1016/j.mib.2008.12.006
    KAY, S.; HAHN, S; MAROIS, E.; HAUSE, G.; BONAS, U.: "A Bacterial Effector Acts as a Plant Transcription Factor and Induces a Cell Size Regulator", SCIENCE, vol. 318, 2007, pages 648 - 651, XP009125817
    KEMPF, V.A.; HITZIGER, N.; RIESS, T.; AUTENRIETH, I.B: "Do plant and human pathogens have a common pathogenicity strategy?", TRENDS MICROBIOL, vol. 10, 2002, pages 269 - 275
    KIM, Y.G.; CHA, J.; CHANDRASEGARAN, S.: "Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain", PROC NATL ACAD SCI U S A, vol. 93, 1996, pages 1156 - 1160, XP002116423, DOI: doi:10.1073/pnas.93.3.1156
    LACROIX, B.; TZFIRA, T.; VAINSTEIN, A.; CITOVSKY, V: "A case of promiscuity: Agrobacterium's endless hunt for new partners", TRENDS GENET, vol. 22, 2006, pages 29 - 37, XP028054918, DOI: doi:10.1016/j.tig.2005.10.004
    LESSL, M.; LANKA, E.: "Common mechanisms in bacterial conjugation and Ti- mediated T-DNA transfer to plant cells", CELL, vol. 77, 1994, pages 321 - 324, XP024244731, DOI: doi:10.1016/0092-8674(94)90146-5
    LI, T.; LIU, B.; SPALDING, M.H.; WEEKS, D.P.; YANG, B: "High-efficiency TALEN- based gene editing produces disease-resistant rice", NAT BIOTECHNOL, vol. 30, 2012, pages 390 - 392, XP055086834, DOI: doi:10.1038/nbt.2199
    LLOSA, M.; ROY, C.; DEHIO, C: "Bacterial type IV secretion systems in human disease", MOL MICROBIOL, vol. 73, 2009, pages 141 - 151
    LLOYD, A.; PLAISIER, C.L.; CARROLL, D.; DREWS, G.N: "Targeted mutagenesis using zinc-finger nucleases in Arabidopsis", PROC NATL ACAD SCI USA, vol. 102, 2005, pages 2232 - 2237, XP055008257, DOI: doi:10.1073/pnas.0409339102
    M. M. MAHFOUZ ET AL: "De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, vol. 108, no. 6, 8 February 2011 (2011-02-08), pages 2623 - 2628, XP055007615, ISSN: 0027-8424, DOI: 10.1073/pnas.1019533108
    MAGORI, S.; CITOVSKY, V.: "The role of the ubiquitin-proteasome system in Agrobacterium tumefaciens-mediated genetic transformation of plants", PLANT PHYSIOL, vol. 160, 2012, pages 65 - 71
    MAHFOUZ, M.M.; LI, L.; PIATEK, M; FANG, X.; MANSOUR, H.; BANGARUSAMY, D.K.; ZHU, J.K.: "Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein", PLANT MOL BIOL, vol. 78, 2012, pages 311 - 321, XP035003111, DOI: doi:10.1007/s11103-011-9866-x
    MALI, P.; YANG, L.; ESVELT, K.M.; AACH, J.; GUELL, M; DICARLO, J.E.; NORVILLE, J.E.; CHURCH, G.M.: "RNA-Guided Human Genome Engineering via Cas9", SCIENCE, 2013, XP002723674, DOI: doi:10.1126/science.1232033
    MCCULLEN, C.A.; BINNS, A.N.: "Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer", ANNU REV CELL DEV BIOL, vol. 22, 2006, pages 101 - 127
    MILLER, J.C. ET AL.: "A TALE nuclease architecture for efficient genome editing", NAT BIOTECHNOL, vol. 29, 2011, pages 143 - 148
    MORBITZER, R.; ROMER, P.; BOCH, J.; LAHAYE, T.: "Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors", PROC NATL ACAD SCI U S A, vol. 107, 2010, pages 21617 - 21622, XP055004257, DOI: doi:10.1073/pnas.1013133107
    MOSCOU, M.J.; BOGDANOVE, A.J.: "A simple cipher governs DNA recognition by TAL effectors", SCIENCE, vol. 326, 2009, pages 1501, XP002599998
    PITZSCHKE, A.; HIRT, H.: "New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation", EMBO J, vol. 29, 2010, pages 1021 - 1032
    ROMER, P.; RECHT, S.; STRAUSS, T.; ELSAESSER, J.; SCHORNACK, S.; BOCH, J.; WANG, S; LAHAYE, T.: "Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae", NEW PHY- TOL, vol. 187, 2010, pages 1048 - 1057, XP055033479, DOI: doi:10.1111/j.1469-8137.2010.03217.x
    ROUET, P.; SMIH, F.; JASIN, M.: "Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells", PROC NATL ACAD SCI U S A, vol. 91, 1994, pages 6064 - 6068, XP002005205, DOI: doi:10.1073/pnas.91.13.6064
    SCHEIFFELE, P.; PANSEGRAU, W.; LANKA, E.: "Initiation of Agrobacterium tumefaciens T-DNA processing. Purified proteins VirD and VirD2 catalyze site- and strand-specific cleavage ofsuperhelical T-border DNA in vitro", J BIOL CHEM, vol. 270, 1995, pages 1269 - 1276
    SCHROEDER, G.; SCHUELEIN, R.; QUEBATTE, M.; DEHIO, C.: "Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2011
    SHUKLA, V.K. ET AL.: "Precise genome modification in the crop species Zea mays using zinc-finger nucleases", NATURE, vol. 459, 2009, pages 437 - 441, XP002626698, DOI: doi:10.1038/NATURE07992
    SILHAVY, D.; A. MOLNAR ET AL.: "A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs", EMBO J, vol. 21, no. 12, 2002, pages 3070 - 80
    TING LI ET AL: "TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 39, no. 1, 1 January 2011 (2011-01-01), pages 359 - 372, XP002632807, ISSN: 0305-1048, [retrieved on 20100810], DOI: 10.1093/NAR/GKQ704
    TOMAS CERMAK ET AL: "Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, GB, vol. 39, no. 12, 1 July 2011 (2011-07-01), pages 1 - 11, XP002659530, ISSN: 1362-4962, [retrieved on 20110414], DOI: 10.1093/NAR/GKR218
    TOWNSEND, J.A.; WRIGHT, D.A.; WINFREY, R.J.; FU, F.; MAEDER, M.L.; JOUNG, J.K.; VOYTAS, D.F: "High-frequency modification of plant genes using engineered zinc-finger nucleases", NATURE, vol. 459, 2009, pages 442 - 445, XP002588972, DOI: doi:10.1038/NATURE07845
    TZFIRA, T.; CITOVSKY, V.: "Agrobacterium-mediated genetic transformation of plants: biology and biotechnology", CURR OPIN BIOTECHNOL, vol. 17, 2006, pages 147 - 154
    TZFIRA, T.; VAIDYA, M.; CITOVSKY, V.: "Involvement of targeted proteolysis in plant genetic transformation by Agrobacterium", NATURE, vol. 431, 2004, pages 87 - 92
    ÜLKER, B.; ALLEN, G.C.; THOMPSON, W.F.; SPIKER, S.; WEISSINGER, A.K: "A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants", THE PLANT JOURNAL, vol. 18, 1999, pages 253 - 263
    URNOV, F.D.; REBAR, E.J.; HOLMES, M.C.; ZHANG, H.S.; GREGORY, P.D.: "Genome editing with engineered zinc finger nucleases", NAT REV GENET, vol. 11, 2010, pages 636 - 646, XP008150557, DOI: doi:10.1038/nrg2842
    VOGEL, A.M.; DAS, A.: "Mutational analysis of Agrobacterium tumefaciens virD2: tyrosine 29 is essential for endonuclease activity", J BACTERIOL, vol. 174, 1992, pages 303 - 308
    WEINTHAL D ET AL: "Genome editing in plant cells by zinc finger nucleases", TRENDS IN PLANT SCIENCE, ELSEVIER SCIENCE, OXFORD, GB, vol. 15, no. 6, 1 June 2010 (2010-06-01), pages 308 - 321, XP027078330, ISSN: 1360-1385, [retrieved on 20100601], DOI: 10.1016/J.TPLANTS.2010.03.001
    WRIGHT, D.A.; TOWNSEND, J.A.; WINFREY, R.J., JR.; IRWIN, P.A.; RAJAGOPAL, J.; LONOSKY, P.M.; HALL, B.D.; JONDLE, M.D.; VOYTAS, D.F: "High-frequency homologous recombination in plants mediated by zinc-finger nucleases", PLANT J, vol. 44, 2005, pages 693 - 705, XP008156361, DOI: doi:10.1111/j.1365-313X.2005.02551.x
    Y. ZHANG ET AL: "Transcription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering", PLANT PHYSIOLOGY, vol. 161, no. 1, 2 November 2012 (2012-11-02), pages 20 - 27, XP055070911, ISSN: 0032-0889, DOI: 10.1104/pp.112.205179
    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, vol. 13, 2001, pages 369 - 383, XP001001554, DOI: doi:10.1105/tpc.13.2.369

Cited By (0)

    Publication numberPublication dateAssigneeTitle