Members

BioProduction Engineering Lab Members (Eng. Biol. Res. C) Keiji Nishida

ProfessorKeiji Nishida

Education and Experience

1997-2001
Bachelor of Science, Plant Biology, University of Tokyo
2001-2003
Master of Science, Biological Science, University of Tokyo, Tsuneyoshi Kuroiwa lab
2003-2005
Doctoral Course Students (DC1) Research Fellowship for Young Scientists, the Japan Society for the Promotion of Science (JSPS)
2003-2006
Ph.D., Biological Science, University of Tokyo, Toshiyuki Nagata lab
2005-2008
Postdoctoral fellow (PD) Research Fellowship for Young Scientists, JSPS
2006-2008
Postdoctoral fellow, Rikkyo University, Tsuneyoshi Kuroiwa lab
2008-2010
Postdoctoral Fellowship for Research Abroad, JSPS
2008-2013
Postdoctoral fellow, Harvard Medical School, Pamela Silver lab
2013-2016
Research Associate Professor, Kobe University
2016-present
Professor, Kobe University

Research Interests

I have been interested in evolutionary design of life. My research career began with studying mitochondrial evolution and endosymbiosis with emphasis on the molecular mechanism of how mitochondrial division and segregation is conducted. In an attempt to integrate synthetic biology approach into evolutionary biology, I have demonstrated the emergence of new biological functionality by conferring bio-magnetism to yeast cells. These experiences lead me to realize the need for new technologies that accelerate designing of life system. My current research involves development of new genome editing tools that employs various DNA modification pathways to facilitate semi-rational and evolutionary design of life. The newly developed genome editing tool termed Target-AID enabled base-editing of DNA without cleavage and now is applicable to wide range of organisms.

Awards

  • 2019　Iue Memorial Foundation Award
  • 2017　NISTEP Award (National Institute of Science and Technology Policy)
  • 2007　BSJ Young Botanist Prize, The botanical Society of Japan
  • 2005　Young Scientist award, The Japanese Society of Plant Morphology

Publications

  1. Mitsunobu, H., Kita, Y., Nambu-Nishida, Y., Miyazaki, S., Nakajima, K., Taoka, K., Kondo, A., Nishida, K. (2025/4) Development of a highly efficient base editing system for Lactobacilli to improve probiotics and dissect essential functions Applied Microbiology and Biotechnology, 109(1), 96
  2. Li, A., Mitsunobu, H., Yoshioka, S., Suzuki, T., Kondo, A., Nishida, K. (2022/08) Cytosine base editing systems with minimized off-target effect and molecular size, Nature Communications, 13 4531
  3. Kashojiya, S., Lu, Y., Takayama, M., Komatsu, H., Minh, L., Nishida, K., Shirasawa, K., Miura, K., Nonaka, S., Masuda, J., Kondo, A., Ezura, H., Ariizumi, T. (2022/01) Modification of tomato breeding traits and plant hormone signaling by Target-AID, the genome-editing system inducing efficient nucleotide substitution, Horticulture Research, 9, uhab004
  4. Yuan, S., Kawasaki, S., Abdellatif, I.MY., Nishida, K., Kondo, A., Ariizumi, T., Ezura, H., Miura, K. (2021/04) Efficient base editing in tomato using a highly expressed transient system, Plant Cell Reports, 40(4): 667-676
  5. Nishida, K., Kondo, A. (2021/01) CRISPR-derived genome editing technologies for metabolic engineering, Metabolic Engineering, 63, 141-147
  6. Hanziker, J., Nishida, K., Kondo, A., Kishimoto, S., Ariizumi, T., Ezura, H. (2020/11) Multiple gene substitution by Target-AID base-editing technology in tomato, Scientific Reports, 10(1), 20471
  7. Shimatani, Z.*, Fujikura, U.*, Ishii, H., Matsui, Y., Suzuki, M., Ueke, Y., Taoka, K., Terada, R., Nishida, K., Kondo, A. (2018/10) Inheritance of co-edited genes by CRISPR-based targeted nucleotide substitutions in rice, Plant Physiology and Biochemistry, 131: 78-83
  8. Arazoe, T., Kondo, A., Nishida, K. (2018/09) Targeted nucleotide editing technologies for microbial metabolic engineering, Biotechnology Journal, 13(9), 1700596
  9. Shimatani, Z., Fujikura, U., Ishii, H., Terada, R., Nishida, K., Kondo, A. (2018/08) Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice, Data in Brief, 20: 1325-1331
  10. Nambu-Nishida, Y., Nishida, K., Hasunuma, T., Kondo, A. (2018/04) Genetic and physiological basis for antibody production by Kluyveromyces marxianus, AMB Express, 8: 56
  11. Banno, S., Nishida, K., Arazoe, T., Mitsunobu, H., Kondo, A. (2018/04) Deaminase-mediated multiplex genome editing in Escherichia coli, Nature Microbiology, 3, 423-429
  12. Yoshida, Y., Kuroiwa, H., Shimada, T., Yoshida, M., Ohnuma, M., Fujiwara, T., Imoto, Y., Yagisawa, F., Nishida, K., Hirooka, S., Misumi, O., Mogi, Y., Akakabe, Y., Matsushita, K., Kuroiwa, T. (2017/12) Glycosyltransferase MDR1 assembles a dividing ring for mitochondrial proliferation comprising polyglucan nanofilaments, Proceedings of the National Academy of Sciences of the United States of America, 114(50), 13284-13289
  13. Mitsunobu, H., Teramoto, J., Nishida, K., Kondo, A. (Review)(2017/10) Beyond native Cas9: manipulating genomic information and function, Trends in Biotechnology, 35(10), 983-996
  14. Nambu-Nishida, Y., Nishida, K., Hasunuma, T., Kondo, A. (2017/08) Development of a comprehensive set of tools for genome engineering in a cold- and thermo-tolerant Kluyveromyces marxianus yeast strain, Scientific Reports, 7(1): 8993
  15. Arazoe, T., Nishida, K., Kondo, A. (2017/06) Targeted nucleotide substitution in mammalian cell by Target-AID, Bio-protocol, 7: 11
  16. 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., Kondo, A. (2017/05) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion, Nature Biotechnology, 35(5), 441-443
  17. Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, Y. K., Shimatani, Z., Kondo, A. (2016/09) Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems., Science,353, aaf8729
  18. Hara, K.Y., Aoki, N., Kobayashi, J., Kiriyama, K., Nishida K., Araki, M., Kondo, A. (2015/11) Improvement of oxidized glutathione fermentation by thiol redox metabolism engineering in Saccharomyces cerevisiae., Applied Microbiology and Biotechnology, 99(22), 9771-9778
  19. Ye, X., Morikawa, K., Ho, S.H., Nishida K., Araki, M., Hasunuma, T., Hara, K.Y., Kondo, A. (2015/04) Evaluation of genes involved in oxidative phosphorylation in yeast by developing a simple and rapid method to measure mitochondrial ATP synthetic activity, Microbial Cell Factories, 14: 56
  20. Yagisawa, F., Fujiwara, T., Ohnuma, M., Kuroiwa, H., Nishida, K., Imoto, Y., Yoshida, Y., Kuroiwa, T. (2013/08) Golgi inheritance in the primitive red alga, Cyanidioschyzon merolae, Protoplasma, 250(4), 943-948
  21. Imoto, Y., Kuroiwa, H., Yoshida, Y., Ohnuma, M., Fujiwara, T., Yoshida, M., Nishida, K., Yagisawa, F., Hirooka, S., Miyagishima, SY., Misumi, O., Kawano, S., Kuroiwa, T. (2013/06) Single-membrane-bounded peroxisome division revealed by isolation of dynamin-based machinery, Proceedings of the National Academy of Sciences of the United States of America, 110(23): 9583-8
  22. Yagisawa, F., Fujiwara, T., Kuroiwa, H., Nishida, K., Imoto, Y., Kuroiwa, T. (2012/10) Mitotic inheritance of endoplasmic reticulum in the primitive red alga Cyanidioschyzon merolae, Protoplasma, 249(4): 1129-35
  23. Nishida, K., Silver, PA. (2012/02) Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway, Plos Biology, 10(2): e1001269, Editors pick of the journal, highlighted in Nature Methods, and cited by several public news articles as "Magnetic yeast"
  24. Imoto, Y., Nishida, K., Yagisawa, F., Yoshida, Y., Ohnuma, M., Yoshida, M., Fujiwara, T., Kuroiwa, H., Kawano, S., Kuroiwa, T. (2011/12) Involvement of Elongation Factor-1α in Cytokinesis without Actomyosin Contractile Ring in the Primitive Red Alga Cyanidioschyzon merolae, Cytologia, 76(4): 431-437
  25. Fujiwara, T., Yagisawa, F., Ohnuma, M., Yoshida, Y., Yoshida, M., Nishida, K., Misumi, O., Kuroiwa, H., Kuroiwa, T. (2010/06) The Vacuole Binding to Mitochondria by VIG1 Contributes an Equal Inheritance of the Vacuoles in Cyanidioschyzon merolae, Cytologia, 75(2): 189-194
  26. Fujiwara, T., Kuroiwa, H., Yagisawa, F., Ohnuma, M., Yoshida, Y., Yoshida, M., Nishida, K., Misumi, O., Watanabe, S., Tanaka, K., Kuroiwa, T. (2010/03) The coiled-coil protein VIG1 is essential for tethering vacuoles to mitochondria during vacuole inheritance of Cyanidioschyzon merolae, Plant Cell, 22(3): 772-81
  27. Hirooka, S., Misumi, O., Yoshida, M., Mori, T., Nishida, K., Yagisawa, F., Yoshida, Y., Fujiwara, T., Kuroiwa, H., Kuroiwa, T. (2009/12) Expression of the Cyanidioschyzon merolae stromal ascorbate peroxidase in Arabidopsis thaliana enhances thermotolerance, Plant Cell Rep, 28(12): 1881-93
  28. Yagisawa, F., Nishida, K., Yoshida, M., Ohnuma, M., Shimada, T., Fujiwara, T., Yoshida, Y., Misumi, O., Kuroiwa, H., Kuroiwa, T. (2009/12) Identification of novel proteins in isolated polyphosphate vacuoles in the primitive red alga Cyanidioschyzon merolae, Plant Journal, 60(5): 882-93
  29. Fujiwara, T., Misumi, O., Tashiro, K., Yoshida, Y., Nishida, K., Yagisawa, F., Imamura, S., Yoshida, M., Mori, T., Tanaka, K., Kuroiwa, H., Kuroiwa, T. (2009/02) Periodic gene expression patterns during the highly synchronized cell nucleus and organelle division cycles in the unicellular red alga Cyanidioschyzon merolae, DNA Research, 16(1): 59-72
  30. Yoshida, Y., Nishida, K., Kuroiwa, T., Kawano, S. (2008/06) Novel Dynamics of FtsZ Ring Before Plastid Abscission, Cytologia, 73(1): 197-201
  31. Misumi, O., Yoshida, Y., Nishida, K., Fujiwara, T., Sakajiri, T., Hirooka, S., Nishimura, Y., Kuroiwa, T. (2008/01) Genome analysis and its significance in four unicellular algae, Cyanidioschyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana, Journal Plant Research, 121(1): 3-17
  32. Yagisawa, F., Nishida, K., Kuroiwa, H., Nagata, T., Kuroiwa, T. (2007/09) Identification and mitotic partitioning strategies of vacuoles in the unicellular red alga Cyanidioschyzon merolae, Planta, 226(4): 1017-29
  33. Nozaki, H., Takano, H., Misumi, O., Terasawa, K., Matsuzaki, M., Maruyama, S., Nishida, K., Yagisawa, F., Yoshida, Y., Fujiwara, T., Takio, S., Tamura, K., Chung, SJ., Nakamura, S., Kuroiwa, H., Tanaka, K., Sato, N., Kuroiwa, T. (2007/07) A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae, BMC Biology, 5: 28
  34. Nishida, K., Yagisawa, F., Kuroiwa, H., Yoshida, Y., Kuroiwa, T. (2007/03) WD40 protein Mda1 is purified with Dnm1 and forms a dividing ring for mitochondria before Dnm1 in Cyanidioschyzon merolae, Proceedings of the National Academy of Sciences of the United States of America, 104(11): 4736-41
  35. Yoshida, Y., Kuroiwa, H., Misumi, O., Nishida, K., Yagisawa, F., Fujiwara, T., Nanamiya, H., Kawamura, F., Kuroiwa, T. (2006/09) Isolated chloroplast division machinery can actively constrict after stretching, Science, 313(5792): 1435-8
  36. Yagisawa, F., Nishida, K., Kuroiwa, H., Nagata, T., Kuroiwa, T. (2005/09) Identification of Lysosome-like Structures in a Unicellular Red Alga Cyanidioschyzon merolae, Cytologia, 70(1): 351-354
  37. Nishida, K., Yagisawa, F., Kuroiwa, H., Nagata, T., Kuroiwa, T. (2005/05) Cell Cycle-regulated, Microtubule-independent Organelle Division in Cyanidioschyzon merolae, Molecular Biology of the Cell, 16(5): 2493-502
  38. Misumi, O., Matsuzaki, M., Nozaki, H., Miyagishima, SY., Mori, T., Nishida, K., Yagisawa, F., Yoshida, Y., Kuroiwa, H., Kuroiwa, T. (2005/02) Cyanidioschyzon merolae genome. A tool for facilitating comparable studies on organelle biogenesis in photosynthetic eukaryotes, Plant Physiology, 137(2): 567-85
  39. Nishida, K., Misumi, O., Yagisawa, F., Kuroiwa, H., Nagata, T., Kuroiwa, T. (2004/07) Triple immunofluorescent labeling of FtsZ, dynamin, and EF-Tu reveals a loose association between the inner and outer membrane mitochondrial division machinery in the red alga Cyanidioschyzon merolae, Journal of Histochemistry & Cytochemistry, 52(7): 843-9
  40. Matsuzaki, M., Misumi, O., Shin-I, T., Maruyama, S., Takahara, M., Miyagishima, SY., Mori, T., Nishida, K., Yagisawa, F., Nishida, K., Yoshida, Y., Nishimura, Y., Nakao, S., Kobayashi, T., Momoyama, Y., Higashiyama, T., Minoda, A., Sano, M., Nomoto, H., Oishi, K., Hayashi, H., Ohta, F,, Nishizaka, S., Haga, S., Miura, S., Morishita, T., Kabeya, Y., Terasawa, K., Suzuki, Y., Ishii, Y., Asakawa, S., Takano, H., Ohta, N., Kuroiwa, H., Tanaka, K., Shimizu, N., Sugano, S., Sato, N., Nozaki, H., Ogasawara, N., Kohara, Y., Kuroiwa, T. (2004/04) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D, Nature, 428(6983): 653-7
  41. Yagisawa, F., Nishida, K., Okano, Y., Minoda, A., Tanaka, K., Kuriowa, T. (2004/03) Isolation of Cycloheximide-resistant mutants of Cyanidioschyzon merolae, Cytologia, 69(1): 97-100
  42. Miyagishima, SY., Nozaki, H., Nishida, K., Nishida. K., Matsuzaki, M., Kuroiwa, T. (2004/03) Two types of FtsZ proteins in mitochondria and red-lineage chloroplasts: the duplication of FtsZ is implicated in endosymbiosis, Journal of Molecular Evolution, 58(3):291-303
  43. Miyagishima, SY., Nishida, K., Mori, T., Matsuzaki, M., Higashiyama, T., Kuroiwa, H., Kuroiwa, T. (2003/03) A plant-specific dynamin-related protein forms a ring at the chloroplast division site, Plant Cell, 15(3): 655-65
  44. Nishida, K., Takahara, M., Miyagishima, SY., Kuroiwa, H., Matsuzaki, M., Kuroiwa, T. (2003/02) Dynamic recruitment of dynamin for final mitochondrial severance in a primitive red alga, Proceedings of the National Academy of Sciences of the United States of America, 100(4): 2146-51

Reviews & Commentaries

  1. 西田敬二, 近藤昭彦, 最新のゲノム編集技術と用途展開, 第3編：微生物への応用と用途展開, 第9章 バクテリアでのゲノム編集の有用性, シーエムシー出版, 79-83 (2021/02)
  2. 大西美輪, 光延仁志, 西田敬二, 最新のゲノム編集技術と用途展開, 第2編：ゲノム編集ツールの開発動向, 第5章 DNA二重鎖切断を伴なわない塩基編集技術, シーエムシー出版, 43-50 (2021/02)
  3. 西田敬二，進展するゲノム編集, 現代化学, 1月号, No.562, ＜特集＞生命をつくる：ゲノム編集の時代, 26-29 (2018/01)
  4. 西田 敬二, 島谷 善平, 近藤 昭彦, デアミナーゼを用いたゲノム編集, 植物の生長調節 (2017/06) 52(1), 15-18
  5. 西田敬二，第1章 3)　切断を伴わないゲノム編集ツール開発（デアミナーゼ他），『All About ゲノム編集』実験医学増刊号， 34(20), 羊土社，35-41 (2016/12)
  6. 近藤昭彦，西田敬二，荒添貴之，第3章　微生物でのゲノム編集の利用と拡大技術，ゲノム編集入門，裳華房，40-55 (2016/12)
  7. Kuroiwa T, Nishida K, Yoshida Y, Fujiwara T, Mori T, Kuroiwa H, Misumi O. Structure, function and evolution of the mitochondrial division apparatus. Biochimica et Biophysica Acta, 1763(5-6):510-21 (2006/05)
  8. Nishida K, Nagata T, Kuroiwa T. Cell cycle regulated organelles division in a primitive red alga. Plant Morphology, 17(1);51-55. (2005)
  9. Miyagishima SY, Nishida K, Kuroiwa T. An evolutionary puzzle: chloroplast and mitochondrial division rings. Trends in Plant Science, 8(9):432-8 (2003/09)