Title:
DNA BINDING PROTEIN USING PPR MOTIF, AND USE THEREOF
Document Type and Number:
WIPO Patent Application WO/2014/175284
Kind Code:
A1
Abstract:
[Problem] Based on the prediction that the rules for DNA recognition possessed by a PPR motif may also be used in DNA recognition, perform analysis of PPR protein that is active in DNA binding, and search for a PPR protein that has such characteristics. The present invention addresses the aforementioned problem by means of a protein that can bind DNA base-selectively or DNA base sequence-specifically, and that contains a plurality of, preferably 2-30, more preferably 5-25, and even more preferably 9-15, PPR motifs having the structure in formula 1 (in formula 1: Helix A is a part that can form an α helix structure; X is a part that does not exist or that comprises 1-9 amino acids; Helix B is a part that can form an α helix structure; and L is a part that comprises 2-7 amino acids), the PPR motif having a specific combination of three amino acids corresponding to the DNA base or target base sequence: first A.A. of Helix A and the 4th A.A. of Helix A in formula 1, together with the "ii"(-2)th A.A. contained in L. (Helix A)-X-(Helix B)-L (formula 1)
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Inventors:
YAMAMOTO TAKASHI (JP)
SAKUMA TETSUSHI (JP)
NAKAMURA TAKAHIRO (JP)
YAGI YUSUKE (JP)
OKAWA YASUYUKI (JP)
SAKUMA TETSUSHI (JP)
NAKAMURA TAKAHIRO (JP)
YAGI YUSUKE (JP)
OKAWA YASUYUKI (JP)
Application Number:
PCT/JP2014/061329
Publication Date:
October 30, 2014
Filing Date:
April 22, 2014
Export Citation:
Assignee:
UNIV KYUSHU NAT UNIV CORP (JP)
UNIV HIROSHIMA (JP)
UNIV HIROSHIMA (JP)
International Classes:
C07K4/10; C07K14/415; C07K19/00; C12N9/16; C12Q1/68
Domestic Patent References:
| WO2011111829A1 | 2011-09-15 | |||
| WO2013058404A1 | 2013-04-25 | |||
| WO2011072246A2 | 2011-06-16 | |||
| WO2011111829A1 | 2011-09-15 |
Foreign References:
| JP2012077274W | 2012-10-22 | |||
| JP2011242250A | 2011-12-01 |
Other References:
IKEDA T.M. ET AL.: "Characterization of a DNA- binding Protein Implicated in Transcription in Wheat Mitochondria", MOLECULAR AND CELLULAR BIOLOGY, vol. 19, no. 12, December 1999 (1999-12-01), pages 8113 - 8122, XP055293993
KOUSSEVIZKY S. ET AL.: "Signals from Chloroplasts Converge to Regulate Nuclear Gene Expression", SCIENCE, vol. 316, 2007, pages 715 - 719, XP055293994
PFALZ J. ET AL.: "pTAC2 to 6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression", THE PLANT CELL, vol. 18, 2006, pages 176 - 197, XP055293997
CHI W. ET AL.: "The Pentratricopeptide Repeat Protein DELAYED GREENING1 is Involved in the Regulation of Early Chloroplast Development and Chloroplast Gene Expression in Arabidopsis", PLANT PHYSIOLOGY, vol. 147, 2008, pages 573 - 584, XP055293999
DING YH. ET AL.: "Arabidopsis GLUTAMINE-RICH PROTEIN23 Is Essential for Early Embryogenesis and Encodes a Novel Nuclear PPR Motif Protein That Interacts with RNA Polymerase II Subunit III", PLANT CELL, vol. 18, 2006, pages 815 - 830, XP055294000
KOBAYASHI K ET AL.: "Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein", NUCLEIC ACIDS RES., vol. 40, no. 6, March 2012 (2012-03-01), pages 2712 - 2723, XP055064492
BARKAN A ET AL.: "A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins", PLOS GENET., vol. 8, no. 8, 16 August 2012 (2012-08-16), pages E1002910, XP003031019
YAGI Y. ET AL.: "Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants", PLOS ONE, vol. 8, no. ISSUE., 5 March 2013 (2013-03-05), pages E57286, XP055172927
YUSUKE YAGI ET AL.: "PPR motif as a new DNA/RNA binding module for genome editing", THE MOLECULAR BIOLOGY SOCIETY OF JAPAN NENKAI PROGRAM YOSHISHU, vol. 36 TH, 20 November 2013 (2013-11-20), pages 2P-1016, XP008183362
MAEDER, M.L. ET AL.: "Rapid ''open-source'' engineering of customized zinc-finger nucleases for highly efficient gene modification", MOL. CELL, vol. 31, 2008, pages 294 - 301, XP055143755, DOI: doi:10.1016/j.molcel.2008.06.016
UMOV, F.D. ET AL.: "Genome editing with engineered zinc finger nucleases", NATURE REVIEW GENETICS, vol. 11, 2010, pages 636 - 646
MILLER, J.C. ET AL.: "A TALE nuclease architecture for efficient genome editing", NATURE BIOTECH., vol. 29, 2011, pages 143 - 148
MALI P ET AL.: "RNA-guided human genome engineering via Cas9", SCIENCE, vol. 339, 2013, pages 823 - 826
CONG L. ET AL.: "2013) Multiplex genome engineering using CRISPR/Cas systems", SCIENCE, vol. 339, pages 819 - 823, XP055400719, DOI: doi:10.1126/science.1231143
SMALL, I.D.; PEETERS, N: "The PPR motif - a TPR-related motif prevalent in plant organellar proteins", TRENDS BIOCHEM. SCI, vol. 25, 2000, pages 46 - 47, XP002311887
WOODSON, J.D.; D CHORY, J.: "Coordination of gene expression between organellar and nuclear genomes", NATURE REV. GENET., vol. 9, 2008, pages 383 - 395
WANG, X. ET AL.: "Modular recognition of RNA by a human pumilio-homology domain", CELL, vol. 110, 2002, pages 501 - 512
CHEONG, C.G; HALL AND T.M.: "Engineering RNA sequence specificity ofPumilio repeats", PROC. NATL. ACAD. SCI. USA, vol. 103, 2006, pages 13635 - 13639, XP002573354, DOI: doi:10.1073/pnas.0606294103
IKEDA T.M.; GRAY M.W.: "Characterization of a DNA-binding protein implicated in transcription in wheat mitochondria", MOL. CELL BIO., vol. 119, no. 12, 1999, pages 8113 - 8122, XP055293993, DOI: doi:10.1128/MCB.19.12.8113
KOUSSEVITZKY S. ET AL.: "Signals from chloroplasts converge to regulate nuclear gene expression", SCIENCE, vol. 316, 2007, pages 715 - 719, XP055293994, DOI: doi:10.1126/science. 1140516
PFALZ J ET AL.: "PTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression", PLANT CELL, vol. 18, 2006, pages 176 - 197, XP055293997, DOI: doi:10.1105/tpc.105.036392
CHI W ET AL.: "The pentatricopeptide repeat protein DELAYED GREENINGI is involved in the regulation of early chloroplast developmen", PLANT PHYSIO!., vol. 147, 2008, pages 573 - 584
DING YH ET AL.: "Arabidopsis GLUTAMINE-RICH PROTEIN 23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNApolymerase II subunit", PLANT CELL, vol. 18, 2006, pages 815 - 830, XP055294000, DOI: doi:10.1105/tpc.105.039495
KOBAYASHI K ET AL., NUCLEIC ACIDS RES., vol. 40, 2012, pages 2712 - 2723
YAGI, Y ET AL., PLOS ONE, vol. 8, 2013, pages E57286
See also references of EP 3020722A4
KOUSSEVIZKY S. ET AL.: "Signals from Chloroplasts Converge to Regulate Nuclear Gene Expression", SCIENCE, vol. 316, 2007, pages 715 - 719, XP055293994
PFALZ J. ET AL.: "pTAC2 to 6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression", THE PLANT CELL, vol. 18, 2006, pages 176 - 197, XP055293997
CHI W. ET AL.: "The Pentratricopeptide Repeat Protein DELAYED GREENING1 is Involved in the Regulation of Early Chloroplast Development and Chloroplast Gene Expression in Arabidopsis", PLANT PHYSIOLOGY, vol. 147, 2008, pages 573 - 584, XP055293999
DING YH. ET AL.: "Arabidopsis GLUTAMINE-RICH PROTEIN23 Is Essential for Early Embryogenesis and Encodes a Novel Nuclear PPR Motif Protein That Interacts with RNA Polymerase II Subunit III", PLANT CELL, vol. 18, 2006, pages 815 - 830, XP055294000
KOBAYASHI K ET AL.: "Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein", NUCLEIC ACIDS RES., vol. 40, no. 6, March 2012 (2012-03-01), pages 2712 - 2723, XP055064492
BARKAN A ET AL.: "A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins", PLOS GENET., vol. 8, no. 8, 16 August 2012 (2012-08-16), pages E1002910, XP003031019
YAGI Y. ET AL.: "Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants", PLOS ONE, vol. 8, no. ISSUE., 5 March 2013 (2013-03-05), pages E57286, XP055172927
YUSUKE YAGI ET AL.: "PPR motif as a new DNA/RNA binding module for genome editing", THE MOLECULAR BIOLOGY SOCIETY OF JAPAN NENKAI PROGRAM YOSHISHU, vol. 36 TH, 20 November 2013 (2013-11-20), pages 2P-1016, XP008183362
MAEDER, M.L. ET AL.: "Rapid ''open-source'' engineering of customized zinc-finger nucleases for highly efficient gene modification", MOL. CELL, vol. 31, 2008, pages 294 - 301, XP055143755, DOI: doi:10.1016/j.molcel.2008.06.016
UMOV, F.D. ET AL.: "Genome editing with engineered zinc finger nucleases", NATURE REVIEW GENETICS, vol. 11, 2010, pages 636 - 646
MILLER, J.C. ET AL.: "A TALE nuclease architecture for efficient genome editing", NATURE BIOTECH., vol. 29, 2011, pages 143 - 148
MALI P ET AL.: "RNA-guided human genome engineering via Cas9", SCIENCE, vol. 339, 2013, pages 823 - 826
CONG L. ET AL.: "2013) Multiplex genome engineering using CRISPR/Cas systems", SCIENCE, vol. 339, pages 819 - 823, XP055400719, DOI: doi:10.1126/science.1231143
SMALL, I.D.; PEETERS, N: "The PPR motif - a TPR-related motif prevalent in plant organellar proteins", TRENDS BIOCHEM. SCI, vol. 25, 2000, pages 46 - 47, XP002311887
WOODSON, J.D.; D CHORY, J.: "Coordination of gene expression between organellar and nuclear genomes", NATURE REV. GENET., vol. 9, 2008, pages 383 - 395
WANG, X. ET AL.: "Modular recognition of RNA by a human pumilio-homology domain", CELL, vol. 110, 2002, pages 501 - 512
CHEONG, C.G; HALL AND T.M.: "Engineering RNA sequence specificity ofPumilio repeats", PROC. NATL. ACAD. SCI. USA, vol. 103, 2006, pages 13635 - 13639, XP002573354, DOI: doi:10.1073/pnas.0606294103
IKEDA T.M.; GRAY M.W.: "Characterization of a DNA-binding protein implicated in transcription in wheat mitochondria", MOL. CELL BIO., vol. 119, no. 12, 1999, pages 8113 - 8122, XP055293993, DOI: doi:10.1128/MCB.19.12.8113
KOUSSEVITZKY S. ET AL.: "Signals from chloroplasts converge to regulate nuclear gene expression", SCIENCE, vol. 316, 2007, pages 715 - 719, XP055293994, DOI: doi:10.1126/science. 1140516
PFALZ J ET AL.: "PTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression", PLANT CELL, vol. 18, 2006, pages 176 - 197, XP055293997, DOI: doi:10.1105/tpc.105.036392
CHI W ET AL.: "The pentatricopeptide repeat protein DELAYED GREENINGI is involved in the regulation of early chloroplast developmen", PLANT PHYSIO!., vol. 147, 2008, pages 573 - 584
DING YH ET AL.: "Arabidopsis GLUTAMINE-RICH PROTEIN 23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNApolymerase II subunit", PLANT CELL, vol. 18, 2006, pages 815 - 830, XP055294000, DOI: doi:10.1105/tpc.105.039495
KOBAYASHI K ET AL., NUCLEIC ACIDS RES., vol. 40, 2012, pages 2712 - 2723
YAGI, Y ET AL., PLOS ONE, vol. 8, 2013, pages E57286
See also references of EP 3020722A4
Attorney, Agent or Firm:
SIKS & CO. (Kyobashi-Nisshoku Bldg. 8-7, Kyobashi 1-chome, Chuo-k, Tokyo 31, JP)
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