| 1. |
Takahiro Nakamura, PPR protein-based transcriptome editing
, JAACT, 2023.11. |
| 2. |
T Nakamura, Y Yagi, Designer RNA binding protein based on PPR protein, as a new modality for targeted therapy, ESCGT2019, 2019.10. |
| 3. |
中村崇裕, PPR motif as a New DNA/RNA Binding Module for Genome/Transcriptome Editing
, AFELiSA, 2017.11. |
| 4. |
Takahiro Nakamura, PPR motif as a new module for genome and transcriptome editing-from organelle biology to protein engineering-, 2016.02, The pentatricopeptide repeat (PPR) protein family is a eukaryotic specific protein family that is specially expanded in plant (~500), whereas very few in other organisms (five in yeast and six in human). Most PPR proteins are gene-specific regulators of mitochondria and chloroplast gene expression, suggesting that PPR protein is evolved for control of endosymbiotic organelle genome. PPR proteins function as sequence-specific RNA/DNA binding proteins in various RNA/DNA metabolisms including RNA cleavage, splicing, RNA editing, and translation, through recognition by tandem arrays of degenerate 35-amino-acid repeating units, the PPR motifs. Recently, we have cracked the RNA/DNA recognition code: one PPR motif corresponds to one nucleotide, and amino acid variances at three particular positions confer the nucleotide specificity with programmable manner, and further above principles could be applied for both RNA- and DNA-binding PPR proteins. Our finding opened another possibility, the use of PPR motif on “genome editing” (DNA manipulation) and “transcriptome editing” (RNA manipulation). I would like to present current perspective about PPR protein family in endosymbiotic genome regulation, and our recent activities of PPR engineering for genome and transcriptome editing.. |
| 5. |
Takahiro Nakamura, PPR motif as a New DNA/RNA Binding Modulefor Genome/transcriptome Editing, International Symposium on Plant Genome Engineering, 2015.11, Determination of complete genome sequences (DNA) and the transcriptome (RNA) for a wide variety of organisms have opened a new biological era for understanding of the complex genetic functions that define living entities. New technologies have recently emerged that enable targeted editing of genomes in diverse systems, by using designer nucleases with programmable, sequence-specific DNA binding modules of ZF finger and TALE protein, and a guide RNA-based CRISPR/CAS9 system. These advances are driving new approaches to many areas including agriculture, biotechnology and studies of genome structure and function. In contract, versatile, programmable RNA binding module that enables manipulation of a single specific RNA in the living cell, is not available to date.
The PPR (pentatricopeptide repeat) motif-containing protein, that organizes a large family in plants, is a sequence-specific RNA or DNA binding protein involving in multiple aspects of organelle RNA/DNA metabolisms including RNA stability, processing, RNA editing, and transcription. PPR proteins consist of a tandem array of PPR motifs (degenerated 35 amino acids) in variety repeat length (2-27 repeats).
Recently, we cracked the RNA/DNA recognition code: one PPR motif corresponds to one nucleotide, and amino acid variances at three particular positions confer the nucleotide specificity with programmable manner, and the code can be shared between RNA- and DNA-binding PPR proteins. Here we show our recent progress and future perspective of the PPR protein engineering for genome and transcriptome editing.
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| 6. |
Takahiro Nakamura, PPR motif as a New DNA/RNA Binding Modulefor Genome/transcriptome Editing, Conference on Transposition and Genome Engineering 2015, 2015.11, Recently established genome editing technologies using ZF, TALE and CRISPR/Cas9 are driving new approaches to many areas of biotechnology and studies of genome structure and function. In contract, versatile, programmable RNA binding module that enables manipulation of a specific RNA in the living cell, is not available to date. The PPR (pentatricopeptide repeat) motif-containing protein, that organizes a large family in plants, is a sequence-specific RNA/DNA binding protein involving in multiple aspects of organelle gene expression. PPR proteins consist of a tandem array of PPR motifs (35 amino acids) in variety repeat length (2-27 repeats). Using Biochemical and informatics approaches, we successfully cracked the RNA/DNA recognition code: one PPR motif corresponds to one nucleotide, and amino acid variances at three particular positions confer the nucleotide specificity with programmable manner, and further above principles could be applied for both RNA- and DNA-binding PPR proteins. Our finding facilitates the use of PPR motif on “genome editing” (DNA manipulation) and “transcriptome editing” (RNA manipulation). We would like to show our recent progress and future perspective for the PPR protein engineering for genome and transcriptome editing. . |
| 7. |
Takahiro Nakamura, PPR Motifs and Their Engineering, Gordon Research Conference, Reengineering Photosynthetic Organelles, 2015.01. |
| 8. |
Takahiro Nakamura, PPR motif as a new RNA/DNA binding module for genome editing, JAACT2014 Symposium, 2014.11. |
| 9. |
Takahiro Nakamura, Molecular basis for the RNA recognition of the pentatricopeptide repeat (PPR) protein
, The 2nd Meeting on RNA and Biofunctions-Asia Study “RNA Biofunctions and Viruses”, 2013.01. |
| 10. |
Takahiro Nakamura, Molecular basis for the RNA recognition of the pentatricopeptide repeat protein, Frontiers in Plant RNA research 2012, 2012.10. |
