Creation of self-evolving enzymatic system that enables semi rational design of genome

• Project/Area Number: 16K14654
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: System genome science
• Research Institution: Kobe University
• Principal Investigator: NISHIDA KEIJI 神戸大学, 科学技術イノベーション研究科, 教授 (10620338)
• Project Period (FY): 2016-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: ゲノム編集 / 進化 / 人工進化 / 合成生物 / Targegt-AID / Target-G / Target-AID / CRISPR / Cas9 / 合成生物学 / グリコシラーゼ

Outline of Final Research Achievements

The aim of this study is to develop self-evolving genomic system by using a modified DNA glycosylase which induce targeted random mutations at specific genomic locus. To characterize each DNA glycosylases from different sources, orthologs from yeast, bacteria, virus and plants were isolated, fused to CRISPR-dCas9 system and targeted. These were then expressed in yeast cells to assess specific mutagenesis at a genomic locus, showing distinct mutational spectra. By choosing one from these characterized, now region and speed of evolution can be controlled at more ordered manner.

Research Products

• [Journal Article] Genetic and physiological basis for antibody production by Kluyveromyces marxianus (2018)
  • Author(s): Nambu-Nishida Yumiko、Nishida Keiji、Hasunuma Tomohisa、Kondo Akihiko
  • Journal Title: AMB Express Volume: 8 Issue: 1 Pages: 56-56
  • DOI: 10.1186/s13568-018-0588-1
  • NAID: 120006462314
  • Peer Reviewed
• [Journal Article] Deaminase-mediated multiplex genome editing in Escherichia coli (2018)
  • Author(s): Banno S, Nishida K, Arazoe T, Mitsunobu H and Kondo A.
  • Journal Title: Nature Microbiology Volume: 3 Issue: 4 Pages: 423-429
  • DOI: 10.1038/s41564-017-0102-6
  • Peer Reviewed
• [Journal Article] Development of a comprehensive set of tools for genome engineering in a cold- and thermo-tolerant Kluyveromyces marxianus yeast strain (2017)
  • Author(s): Nambu-Nishida Yumiko、Nishida Keiji、Hasunuma Tomohisa、Kondo Akihiko
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 8993-8993
  • DOI: 10.1038/s41598-017-08356-5
  • NAID: 120006346142
  • Peer Reviewed
• [Journal Article] Beyond Native Cas9: Manipulating Genomic Information and Function (2017)
  • Author(s): Mitsunobu Hitoshi、Teramoto Jun、Nishida Keiji、Kondo Akihiko
  • Journal Title: Trends in Biotechnology Volume: 35 Issue: 10 Pages: 983-996
  • DOI: 10.1016/j.tibtech.2017.06.004
• [Journal Article] Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion (2017)
  • Author(s): Shimatani, Z., Kashojiya, S., Takayama, M., Terada, R., Arazoe, T., Ishii, H., Teramura, H., Yamamoto, T., Komatsu, H., Miura, K., Ezura, H., Nishida, K., Ariizumi, T. and Kondo A.
  • Journal Title: Nature Biotechnology Volume: 印刷中 Issue: 5 Pages: 441-443
  • DOI: 10.1038/nbt.3833
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems (2016)
  • Author(s): Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., Shimatani, Z. and Kondo, A.
  • Journal Title: Science Volume: 353 Issue: 6305 Pages: 6305-6305
  • DOI: 10.1126/science.aaf8729
  • Peer Reviewed / Open Access / Int'l Joint Research