Members

BioProduction Engineering Lab Members (Sci., Technol. and Innov.) Jun Ishii

ProfessorJun Ishii

Education and Experience

1998-2002
BSc　Chemical Science and Engineering, Faculty of Engineering, Kobe University, Japan
2002-2004
MSc　Chemical Science and Engineering, Graduate School of Science and Technology, Kobe University, Japan
2004-2008
PhD　Molecular Science and Material Engineering, Graduate School of Science and Technology, Kobe University, Japan
Apr. 2008-Jul. 2008
Postdoctoral fellow, Organization of Advanced Science and Technology, Kobe University, Japan
Aug. 2008-Mar. 2012
Project Assistant Professor, Organization of Advanced Science and Technology, Kobe University, Japan
Apr. 2012-Mar. 2013
Project Associate Professor, Organization of Advanced Science and Technology, Kobe University, Japan
Apr. 2013-Mar. 2016
Associate Professor, Organization of Advanced Science and Technology, Kobe University, Japan
Apr. 2016-Mar.2025
Associate Professor, Graduate School of Science, Technology and Innovation, Kobe University, Japan
Jul. 2018-Mar.2025
Associate Professor, Engineering Biology Research Center, Kobe University, Japan
Apr. 2025-present
Professor, Engineering Biology Research Center, Kobe University, Japan

Publications

  1. Kaneko, S., Fukushima, H., Nakahama, M., Tsuge, K., Ishii, J., Aizawa, Y., Itaya, M., Kondo, A. (2025/09) Versatile Methodology for Efficient Large-sized DNA Delivery Between Microorganisms Without In vitro Purification, Journal of Molecular Biology, 437(17), 169289
  2. Tominaga, M., Kawakami, K., Ogawa, H., Nakamura, T., Kondo, A., Ishii, J. (2025/5) Production of borneol, camphor, and bornyl acetate using engineered Saccharomyces cerevisiae. Metabolic Engineering Communications, 20, e00259
  3. Tominaga, M., Shima, Y., Nozaki, K., Ito, Y., Someda, M., Shoya, Y., Hashii, N., Obata, C., Matsumoto-Kitano, M., Suematsu, K., Matsukawa, T., Hosoya, K., Hashiba, N., Kondo, A., Ishii, J. (2024/12) Designing strong inducible synthetic promoters in yeasts Nature Communications, 15, 10653
  4. Asama, R., Tominaga, M., Ito, S., Ito, Y., Takemura, K., Sakuraba, S., Katsurada, K., Fukuda, N., Kondo, A., Ishii, J.(2024/07) Screening of protein-based inhibitors for the intracellular domain of epidermal growth factor receptor by directed evolution using the yeast Gγ recruitment system, Journal of Bioscience and Bioengineering, 138(5), 375-381
  5. Asama, R., Liu, C.J.S., Tominaga, M., Cheng, Y-R., Nakamura, Y., Kondo, A., Wang, H-Y., Ishii, J. (2024/04) Droplet-based microfluidic platform for detecting agonistic peptides that are self-secreted by yeast expressing a G-protein-coupled receptor, Microbial Cell Factories, 23, 104
  6. Matsuyama, C., Seike, T., Okahashi, N., Niide, T., Hara, KY., Hirono-Hara, Y., Ishii, J., Shimizu, H., Toya, Y., Matsuda, F. (2024/03) Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin, Journal of Bioscience and Bioengineering, 137(3), 187-194
  7. Morita, K., Takenaka, M., Tomita, K., Ishii, J., Kawaguchi, H., Murakami, D., Amo, H., Fujii, M., Maruyama, T., Matsumoto, T., Nishino, T., Ogino, C. (2023/11) Nanoscopic lignin mapping on cellulose nanofibers via scanning transmission electron microscopy and atomic force microscopy. Cellulose, 30: 11357–11367
  8. Sugimura, M., Seike, T., Okahashi, N., Izumi, Y., Bamba, T., Ishii, J., Matsuda F. (2023/11) Improved 2,3-butanediol production rate of metabolically engineered Saccharomyces cerevisiae by deletion of RIM15 and activation of pyruvate consumption pathway. International Journal of Molecular Sciences, 24(22): 16378
  9. Yatabe, F., Seike, T., Okahashi, N., Ishii, J., Matsuda, F. (2023/10) Improvement of ethanol and 2,3-butanediol production in Saccharomyces cerevisiae by ATP wasting. Microbial Cell Factories, 22(1): 204
  10. Arai, T., Wada, M., Nishiguchi, H., Takimura, Y., Ishii, J. (2023/05) Inducer-free recombinant protein production in Trichoderma reesei: secretory production of endogenous enzymes and heterologous nanobodies using glucose as the sole carbon source, Microbial Cell Factories, 22: 103
  11. Takenaka, M., Yoshida, T., Yoshida, E., Ono, S., Horie, S., Vavricka, CJ., Hiratani, M., Tsuge, K., Ishii, J., Hayakawa, Y., Kondo, A., Hasunuma, T. (2023/01) Online SFE-SFC-MS/MS colony screening: a high-throughput approach for optimizing (-)-limonene production, Journal of Chromatography B, 1215, 123588
  12. Morita, K., Nishimura, Y., Ishii, J., Maruyama, T. (2022/12) Micelle-like nanoassemblies of short peptides create antimicrobial selectivity in a conventional antifungal drug. ACS Applied Nano Materials, 6(2): 1432-1440
  13. Otsuka, K., Seike, T., Toya, Y., Ishii, J., Hirono-Hara, Y., Hara, KY., Matsuda, F. (2022/12) Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli, Journal of Bioscience and Bioengineering, 134(6): 484-490
  14. Sano, M., Tanaka, R., Kamata, K., Hirono-Hara, Y., Ishii, J., Matsuda, F., Hara, KY., Shimizu, H., Toya, Y. (2022/11) Conversion of mevalonate to isoprenol using light energy in Escherichia coli without consuming sugars for ATP supply, ACS Synthetic Biology, 11, 3966-3972
  15. Ito, Y., Ishigami, M., Hashiba, N., Nakamura, Y., Terai, G., Hasunuma, T., Ishii, J., Kondo, A. (2022/09) Avoiding entry into intracellular protein degradation pathways by signal mutations increases protein secretion in Pichia pastoris, Microbial Biotechnology, 15(9), 2364-2378
  16. Isogai, S., Tominaga, M., Kondo, A., Ishii, J. (2022/07) Plant flavonoid production in bacteria and yeasts, Frontiers in Chemical Engineering, 4, 880694
  17. Tominaga, M., Miyazaki, K., Hataya, S., Mitsui, Y., Kuroda, S., Kondo, A., Ishii, J. (2022/07) Enhanced squalene production by modulation of pathways consuming squalene and its precursor, Journal of Bioscience and Bioengineering, 134(1), 1-6
  18. Toya, Y., Hirono-Hara, Y., Hirayama, H., Kamata, K., Tanaka, R., Sano, M., Kitamura, S., Otsuka, K., Abe-Yoshizumi, R., Tsunoda, S., Kikukawa, H., Kandori, H., Shimizu, H., Matsuda, F., Ishii, J., Hara, KY. (2022/07) Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems, Metabolic Engineering, 72, 227-236
  19. Ito, Y., Ishigami, M., Terai, G., Nakamura, Y., Hashiba, N., Nishi, T., Nakazawa, H., Hasunuma, T., Asai, K., Umetsu, M., Ishii, J., Kondo, A. (2022/06) A streamlined strain engineering workflow with genome-wide screening detects enhanced protein secretion in Komagataella phaffii, Communications Biology, 5, 561
  20. Tominaga, M., Kondo, A., Ishii, J. (2022/04) (Review) Engineering of Synthetic Transcriptional Switches in Yeast, Life, 12, 557
  21. Morita, K., Seike, T., Ishii, J., Matsuda, F., Shimizu, H. (2022/03) Improvement of 2, 3-butanediol production by dCas9 gene expression system in Saccharomyces cerevisiae, Journal of Bioscience and Bioengineering, 133(3), 208-212
  22. Vavricka, CJ., Takahashi, S., Watanabe, N., Takenaka, M., Matsuda, M., Yoshida, T., Suzuki, R., Kiyota, H., Li, J., Minami, H., Ishii, J., Tsuge, K., Araki, M., Kondo, A., Hasunuma, T. (2022/03) Machine learning discovery of missing links that mediate alternative branches to plant alkaloids, Nature Communications, 13, 1405
  23. Nishi, T., Ito, Y., Nakamura, Y., Yamaji, T., Hashiba, N., Tamai, M., Yasohara, Y., Ishii, J.*, Kondo, A. (2022/01) One-step in vivo assembly of multiple DNA fragments and genomic integration in Komagataella phaffii, ACS Synthetic Biology, 11(2), 644-654
  24. Katsurada, K., Tominaga, M., Kaishima, M., Kato, H., Matsuno, T., Ogino, C., Kondo, A., Ishii, J.*, Takayama, K. (2021/12) Constitutive cell surface expression of ZZ domain for the easy preparation of yeast-based immunosorbents, The Journal of General and Applied Microbiology, 67(6), 265-268
  25. Yoshida, E., Kojima, M., Suzuki, M., Matsuda, F., Shimbo, K., Onuki, A., Nishio, Y., Usuda, Y., Kondo, A., Ishii, J. (2021/11) Increased carvone production in Escherichia coli by balancing limonene conversion enzyme expression via targeted quantification concatamer proteome analysis, Scientific Reports, 11(1): 22126
  26. Isogai, S., Okahashi, N., Asama, R., Nakamura, T., Hasunuma, T., Matsuda, F., Ishii, J.*, Kondo, A.* (2021/06) Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases, Metabolic Engineering Communications, 12, e00169
  27. Shoji, S., Yamaji, T., Makino, H., Ishii, J., Kondo, A. (2021/05) Metabolic design for selective production of nicotinamide mononucleotide from glucose and nicotinamide, Metabolic Engineering, 65, 167-177
  28. Tominaga, M., Nozaki, K., Umeno, D., Ishii, J.*, Kondo, A. (2021/03) Robust and flexible platform for directed evolution of yeast genetic switches, Nature Communications, 12: 1846
  29. Nakamura, Y., Asama, R., Tabata, T., Morita, K., Maruyama, T., Kondo, A., Ishii, J.* (2021/02) Comparative analyses of site-directed mutagenesis of human melatonin MTNR1A and MTNR1B receptors using a yeast fluorescent biosensor, Biotechnology and Bioengineering, 118(2), 863-876
  30. Ito, Y., Terai, G., Ishigami, M., Hashiba, N., Nakamura, Y., Bamba, T., Kumokita, R., Hasunuma, T., Asai, K., Ishii, J.*, Kondo, A.* (2020/12) Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression, Nucleic Acids Research, 48(22), 13000-13012
  31. Nishimura, Y., Ezawa, R., Morita, K., Nakayama, M., Ishii, J., Sasaki, R., Ogino, C., Kondo, A. (2020/09) In vivo evaluation of the ZHER2-BNC/LP carrier encapsulating an anticancer drug and a radiosensitizer, ACS Applied Bio Materials, 3(11), 7743-7751
  32. Morita, K., Matsuda, F., Okamoto, K., Ishii, J., Kondo, A., Shimizu, H. (2019/10) Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae, Microbial Cell Factories, 18, 177
  33. Vavricka, CJ., Yoshida, T., Kuriya, Y., Takahashi, S., Ogawa, T., Ono, F., Agari, K., Kiyota, H., Li, J., Ishii, J., Tsuge, K., Minami, H., Araki, M.*, Hasunuma, T.*, Kondo, A. (2019/05) Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids, Nature Communications, 10, 2015
  34. Tamano, K., Cox Ⅲ, RS., Tsuge, K., Miura, A., Itoh, A., Ishii, J., Tamura, T., Kondo, A., Machida, M. (2019/04) Heterologous production of free dihomo-ɤ-linolenic acid by Aspergillus oryzae and its extracellular release via surfactant supplementation, Journal of Bioscience and Bioengineering, 127, 451-457
  35. Itoh, H., Matsui, M., Miyamura, Y., Takeda, I., Ishii, J., Kumagai, T., Machida, M., Shibata, T., Arita, M. (2018/12) Biosynthesis of Novel Statins by Combining Heterologous Genes from Xylaria and Aspergillus, ACS Synthetic Biology, 7(12), 2783-2789
  36. Ito, Y., Watanabe, T., Aikawa, S., Nishi, T., Nishiyama, T., Nakamura, Y., Hasunuma, T., Okubo, Y., Ishii, J.*, Kondo, A.* (2018/11) Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in Komagataella phaffii, FEMS Yeast Research, 18(7), foy074
  37. Nakamura, Y., Nishi, T., Noguchi, R., Ito, Y., Watanabe, T., Nishiyama, T., Aikawa, S., Hasunuma, T., Ishii, J.*, Okubo, Y., Kondo, A.* (2018/07) A stable, autonomously replicating plasmid vector containing Pichia pastoris centromeric DNA, Applied and Environmental Microbiology, 84(15), e02882-17
  38. Restu, WK., Nishida, Y., Yamamoto, S., Ishii, J., Maruyama, T. (2018/07) Short oligopeptides for biocompatible and biodegradable supramolecular hydrogels. Langmuir, 34, 8065-8074
  39. Ishii, J., Morita, K., Ida, K., Kato, H., Kinoshita, S., Hataya, S., Shimizu, H., Kondo, A., Matsuda, F. (2018/06) A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae, Biotechnology for Biofuels, 11: 180
  40. Hashi, H., Nakamura, Y., Ishii, J.*, Kondo, A. (2018/04) Modifying expression modes of human neurotensin receptor type 1 alters sensing capabilities for agonists in yeast signaling biosensor, Biotechnology Journal, 13(4), e1700522
  41. Nishimura, Y., Matsui, T., Ishii, J., Kondo, A. (2018/03) Metabolic Engineering of the 2-Ketobutyrate Biosynthetic Pathway for 1-Propanol Production in Saccharomyces cerevisiae, Microbial Cell Factories, 17: 38
  42. Nambu-Nishida, Y., Sakihama, Y., Ishii, J., Hasunuma, T., Kondo, A. (2018/01) Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation, Journal of Bioscience and Bioengineering, 125(1), 76-86
  43. A. Prima, Hara, Y. K., A. C. Djohan, Kashiwagi, N., P. Kahar, Ishii, J., Nakayama, H., Okazaki, F., B. Prasetya, Kondo, A., Yopi, Ogino, C. (2017/12) Glutathione production from mannan-based bioresource by mannanase/mannosidase expressing Saccharomyces cerevisiae, Bioresource Technology, 245, 1400-1406
  44. Hara, Y. K., Kobayashi, J., Yamada, R., Sasaki, D., Kuriya, Y., Hirono-Hara, Y., Ishii, J., Araki, M., Kondo, A. (2017/11) Transporter Engineering in Biomass Utilization by Yeast, FEMS Yeast Research, 17(7), fox061
  45. Morita, K., Nomura, Y., Ishii, J., Matsuda, F., Kondo, A., Shimizu, H. (2017/09) Heterologous expression of bacterial phosphoenol pyruvate carboxylase and Entner-Doudoroff pathway in Saccharomyces cerevisiae for improvement of isobutanol production, Journal of Bioscience and Bioengineering, 124(3), 263-270
  46. Fukuda, N., Kaishima, M., Ishii, J., Honda, S. (2017/08) Positive detection of GPCR antagonists using a system for inverted expression of a fluorescent reporter gene. ACS Synthetic Biology, 6(8), 1554-1562
  47. Ryo, S., Ishii, J., Matsuno, T., Nakamura, Y., Matsubara, D., Tominaga, M., Kondo, A. (2017/06) Positive feedback genetic circuit incorporating a constitutively active mutant Gal3 into yeast GAL induction system, ACS Synthetic Biology, 6(6), 928-935
  48. Fukutani, Y., Ishii, J., Kondo, A., Ozawa, T., Matsunami, H., Yohda, M. (2017/06) Split luciferase complementation assay for the analysis of G protein-coupled receptor ligand response in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 114(6): 1354-1361
  49. Nishimura, Y., Ezawa, R., Ishii, J., Ogino, C., Kondo, A. (2017/01) Affibody-displaying bio-nanocapsules effective in EGFR, typical biomarker, expressed in various cancer cells, Bioorganic & Medicinal Chemistry Letters, 27(2), 336-341
  50. Fukuda, N., Kaishima, M., Ishii, J., Kondo, A., Honda, S. (2016/12) Continuous crossbreeding of sake yeasts using growth selection systems for a-type and α-type cells, AMB Express, 6: 45
  51. Inokuma, K., Bamba, T., Ishii, J., Ito, Y., Hasunuma, T., Kondo, A. (2016/11) Enhanced cell-surface display and secretory production of cellulolytic enzymes with Saccharomyces cerevisiae Sed1 signal peptide, Biotechnology and Bioengineering, 113(11), 2358-2366
  52. Kaishima, M., Ishii, J.*, Matsuno, T., Fukuda, N., Kondo, A. (2016/10) Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity, Scientific Reports, 6: 35932
  53. Nakamura, Y., Hashimoto, T., Ishii, J.*, Kondo, A. (2016/10) Dual-color reporter switching system to discern dimer formations of G-protein-coupled receptors using Cre/loxP site-specific recombination in yeast, Biotechnology and Bioengineering, 113(10), 2178-2190
  54. Yamamoto, K., Hara, Y.K., Morita, T., Nishimura, A., Sasaki, D., Ishii, J., Ogino, C., Kizaki, N., Kondo, A. (2016/09) Enhancement of astaxanthin production in Xanthophyllomyces dendrorhous by efficient method for the complete deletion of genes, Microbial Cell Factories, 15(1): 155
  55. Ishii, J., Okazaki, F., Djohan, C. Apridah., Hara, Y.K., Asai-Nakashima, N., Teramura, H., Andriani, A., Tominaga, M., Wakai, S., Kahar, P., Yopi, Prasetya, B., Ogino, C., Kondo, A. (2016/09) From mannan to bioethanol: cell surface co-display of β-mannanase and βmannosidase on yeast Saccharomyces cerevisiae, Biotechnology for Biofuels, 9, 188
  56. Shen, L., Nishimura, Y., Matsuda, F., Ishii, J., Kondo, A. (2016/07) Overexpressing enzymes of the Ehrlich pathway and deleting genes of the competing pathway in Saccharomyces cerevisiae for increasing 2-phenylethanol production from glucose, Journal of Bioscience and Bioengineering, 122(1), 34-39
  57. Nakamura, Y., Ishii, J., Kondo, A. (Review) (2016/05) Current techniques for studying oligomer formations of G-protein-coupled receptors using mammalian and yeast cells, Current Medicinal Chemistry, 23(16), 1638-1656
  58. Hattan, J., Shindo, K., Ito, T., Shibuya, Y., Watanabe, A., Tagaki, C., Ohno, F., Sasaki, T., Ishii, J., Kondo, A., Misawa, N. (2016/04) Identification of a novel hedycaryol synthase gene isolated from Camellia brevistyla flowers andfloral scent of Camellia cultivars, Planta, 243(4), 959-972
  59. Tsuge, Y., Kudou, M., Kawaguchi, H., Ishii, J., Hasunuma, T., Kondo, A. (2016/03) FudC, a protein primarily responsible for furfural detoxification in Corynebacterium glutamicum, Applied Microbiology and Biotechnology, 100(6), 2685-2692
  60. Hiraoka, R., Funasaki, Y., Ishii, J., Maruyama, T. (2015/12) Rational design of degradable polyanion for layer-by-layer assembly for encapsulation and release of cationic functional biomolecules, Chemical Communications, 51(98): 17447-17450
  61. Hasunuma, T., Ishii, J., Kondo, A. (Review) (2015/12) Rational design and evolutional fine tuning of Saccharomyces cerevisiae for biomass breakdown, Current Opinion in Chemical Biology, 29: 1-9
  62. Kaishima, M., Ishii, J.*, Fukuda, N., Kondo, A. (2015/11) Gγ recruitment systems specifically select PPI and affinity-enhanced candidate proteins that interact with membrane protein targets, Scientific Reports, 5, 16723
  63. Nakamura, Y., Ishii, J., Kondo, A. (2015/09) Applications of yeast-based signaling sensor for characterization of antagonist and analysis of site-directed mutants of the human serotonin 1A receptor, Biotechnology and Bioengineering, 112(9), 1906-1915
  64. Ida, K., Ishii, J., Matsuda, F., Kondo, T., Kondo, A. (2015/04) Eliminating the isoleucine biosynthetic pathway to reduce competitive carbon outflow during isobutanol production by Saccharomyces cerevisiae, Microbial Cell Factories, 14: 62
  65. Inokuma, K., Ishii, J., Hara, K.Y., Mochizuki, M., Hasunuma, T., Kondo, A. (2015/04) Complete genome sequence of Kluyveromyces marxianus NBRC1777, a nonconventional thermotolerant yeast, Genome Announcements, 3(2), e00389-15
  66. Takenaka, M., Miyachi, Y., Ishii, J., Ogino, C., Kondo, A. (2015/03) The mapping of yeast's G-protein coupled receptor with an atomic force microscope, Nanoscale, 7, 4956-4963
  67. Mohamed suffian, I.F., Nishimura, Y., Morita, K., Nakamura-Tsuruta, S., Al-Jamal, K.T., Ishii, J., Ogino, C., Kondo, A. (2015/02) Mutation of arginine residues to avoid non-specific cellular uptakes for hepatitis B virus core particles, Journal of Nanobiotechnology, 13(1): 15
  68. Fukutani, Y., Hori, A., Tsukada, S., Sato, R., Ishii, J., Kondo, A., Matsunami, H., Yohda, M. (2015/02) Improving the odorant sensitivity of olfactory receptor-expressing yeast with accessory proteins, Analytical Biochemistry, 471, 1-8
  69. Suzuki, H., Ishii, J., Kondo, A., Yoshida, K. (2015/02) Polyamino acid display on cell surfaces enhances salt and alcohol tolerance of Escherichia coli, Biotechnology Letters, 37(2), 429-435
  70. Inokuma, K., Yoshida, T., Ishii, J., Hasunuma, T., Kondo, A. (2015/02) Efficient co-displaying and artificial ratio control of α-amylase and glucoamylase on the yeast cell surface by using combinations of different anchoring domains, Applied Microbiology and Biotechnology, 99(4), 1655-1663
  71. Nakamura, Y., Ishii, J., Kondo, A. (2014/11) Construction of a yeast-based signaling biosensor for human angiotensin Ⅱtype 1 receptor via functional coupling between Asn295-mutated receptor and Gpa1/Gi3 chimeric Gα, Biotechnology and Bioengineering, 111(11), 2220-2228
  72. Tsuge, Y., Hori, Y., Kudou, M., Ishii, J., Hasunuma, T., Kondo, A. (2014/10) Detoxification of furfural in Corynebacterium glutamicum under aerobic and anaerobic conditions, Applied Microbiology and Biotechnology, 98(20), 8675-8683
  73. Kaishima, M., Fukuda, N., Ishii, J., Kondo, A. (2014/09) Desired alteration of protein affinities: competitive selection of protein variants using yeast signal transduction machinery, PLoS ONE, 9(9): e108229
  74. Nishimura, Y., Ishii, J., Ogino, C., Kondo, A. (Review) (2014/09) Genetic engineering of bio-nanoparticles for drug delivery: a review, Journal of Biomedical Nanotechnology, 10(9), 2063-2085
  75. Nakamura, Y., Ishii, J., Kondo, A. (2014/08) Signaling assays for detection of human G-protein-coupled receptors in yeast, Bio-protocol, 4(16), e1206
  76. Ishii, J., Kondo, T., Makino, H., Ogura, A., Matsuda, F., Kondo, A. (2014/05) Three gene expression vector sets for concurrently expressing multiple genes in Saccharomyces cerevisiae, FEMS Yeast Research, 14(3), 399-411
  77. Nishimura, Y., Takeda, K., Ezawa, R., Ishii, J., Ogino, C., Kondo, A. (2014/04) A display of pH-sensitive fusogenic GALA peptide facilitates endosomal escape from a Bio-nanocapsule via an endocytic uptake pathway, Journal of Nanobiotechnology, 21(1), 11
  78. Nakamura, Y., Takemoto, N., Ishii, J., Kondo, A. (2014/03) Simultaneous method for analyzing dimerization and signaling of G-protein-coupled receptor in yeast by dual-color reporter system, Biotechnology and Bioengineering, 111(3), 586-596
  79. Ishii, J., Oda, A., Togawa, S., Fukao, A., Fujiwara, T., Ogino, C., Kondo, A. (2014/02) Microbial fluorescence sensing for human neurotensin receptor type 1 using Gα-engineered yeast cells, Analytical Biochemistry, 446, 37-43
  80. Matsuda, F., Ishii, J., Kondo, T., Ida, K., Tezuka, H,. Kondo, A. (2013/12) Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance, Microbial Cell Factories, 12: 119
  81. Nakamura, Y., Ishii, J., Kondo, A. (2013/12) Bright fluorescence monitoring system utilizing Zoanthus sp. green fluorescent protein (ZsGreen) for human G-protein-coupled receptor signaling in microbial yeast cells, PLoS ONE, 8(12), e82237
  82. Matsuda, F., Shirai, T., Ishii, J., Kondo, A. (2013/07) Regulation of central carbon metabolism in Saccharomyces cerevisiae by metabolic inhibitors, Journal of Bioscience and Bioengineering, 116(1), 59-64
  83. Nishimura, Y., Mieda, H., Ishii, J., Ogino, Fujiwara, T., Kondo, A. (2013/06) Targeting cancer cell-specific RNA interference by siRNA delivery using a complex carrier of affibody-displaying bio-nanocapsules and liposomes, Journal of Nanobiotechnology, 11, 19
  84. Nakamura, Y., Ishii, J., Kondo, A. (2013/06) Rapid, facile detection of heterodimer partners for target human G-protein-coupled receptors using a modified split-ubiquitin membrane yeast two-hybrid system, PLoS ONE, 8(6), e66793
  85. Hasunuma, T., Okazaki, F., Okai, N., Hara, K.Y., Ishii, J., Kondo, A. (Review) (2013/05) A review of enzymes and microbes for lignocellulosic biorefinery and the possibility of their application to consolidated bioprocessing technology, Bioresourse Technology, 135, 513-522
  86. Nishimura, Y., Takeda, K., Ishii, J., Ogino, C., Kondo, A. (2013/05) An affinity chromatography method used to purify His-tag-displaying bio-nanocapsules, Journal of Virological Methods, 189(2), 393-396
  87. Nishimura, Y., Mimura, W., Suffian, IMF, Amino, T., Ishii, J., Ogino C., Kondo, A. (2013/03) Granting specificity for breast cancer cells using a Hepatitis B core particle with a HER2-targeted affibody molecule, Journal of Biochemistry, 153(3), 251-256
  88. Ishii, J., Yoshimura, K., Hasunuma, T., Kondo, A., (2013/03) Reduction of furan derivatives by overexpressing NADH-dependent Adh1 improves ethanol fermentation using xylose as sole carbon source with Saccharomyces cerevisiae harboring XR-XDH pathway, Applied Microbiology and Biotechnology, 97(6), 2597-2607
  89. Suga, H., Matsuda, F., Hasunuma, T., Ishii, J., Kondo, A. (2013/02) Implementation of a transhydrogenase-like shunt to counter redox imbalance during xylose fermentation in Saccharomyces cerevisiae, Applied Microbiology and Biotechnology, 97(4), 1669-1678
  90. Kondo, A., Ishii, J., Hara, K.Y., Hasunuma, T., Matsuda, F. (Review) (2013/01) Development of microbial cell factories for bio-refinery through synthetic bioengineering, Journal of Biotechnololgy, 163(2), 204-216
  91. Nishimura, Y., Ishii, J., Okazaki, F., Ogino, C., Kondo, A. (2012/12) Complex carriers of affibody-displaying bio-nanocapsules and composition-varied liposomes for HER2-expressing breast cancer cell-specific protein delivery, Journal of Drug Targeting, 20(10), 897-905
  92. Fukutani, Y., Ishii, J., Noguchi, K., Kondo, A., Yohda, M. (2012/12) An improved bioluminescence-based signaling assay for odor sensing with a yeast expressing a chimeric olfactory receptor, Biotechnology and Bioengineering, 109(12), 3143-3151
  93. Matsuda, F., Kondo, T., Ida, K., Tezuka, H., Ishii, J., Kondo, A. (2012/11) Construction of an artificial pathway for isobutanol biosynthesis in the cytosol of Saccharomyces cerevisiae, Bioscience, Biotechnlolgy, and Biochemistry, 76(11), 2139-2141
  94. Ishii, J., Moriguchi, M., Hara, K.Y., Shibasaki, S., Fukuda, H., Kondo, A. (2012/07) Improved identification of agonist-mediated Gα(i)-specific human G-protein-coupled receptor signaling in yeast cells by flow cytometry, Analytical Biochemistry, 426(2), 129-133
  95. Ishii, J., Yoshimoto, N., Tatematsu, K., Kuroda, S., Ogino, C., Fukuda, H., Kondo, A. (2012/05) Cell wall trapping of autocrine peptides for human g-protein-coupled receptors on the yeast cell surface, PLoS ONE, 7(5): e37136
  96. Hara, K.Y., Kim, S., Kiriyama, K., Yoshida, H., Arai, S., Ishii, J., Ogino, C., Fukuda, H., Kondo, A. (2012/05) An energy-saving glutathione production method from low-temperature cooked rice using amylase-expressing Saccharomyces cerevisiae, Biotechnology Journal, 7(5), 686-689
  97. Ryo, S., Ishii, J., Iguchi, Y., Fukuda, N., Kondo, A. (2012/05) Transplantation of the GAL regulon into G-protein signaling circuitry in yeast, Analytical Biochemistry, 424(1), 27-31
  98. Kondo, T., Tezuka, H., Ishii, J., Matsuda, F., Ogino, C., Kondo, A. (2012/05) Genetic engineering to enhance the Ehrlich pathway and alter carbon flux for increased isobutanol production from glucose by Saccharomyhces cerevisiae, Journal of Biotechnology, 159(1-2), 32-7
  99. Nishimura, Y., Shishido, T., Ishii, J., Tanaka, T., Ogino, C., Kondo, A. (2012/01) Protein-encapsulated bio-nanocapsules production with ER membrane localization sequences, Journal of Biotechnology, 157(1), 124-129
  100. Fukutani, Y., Nakamura, T., Yorozu, M., Ishii, J., Kondo, A., Yohda, M. (2012/01) The N-terminal replacement of an olfactory receptor for the development of a yeast-based biomimetic odor sensor, Biotechnology and Bioengineering, 109(1), 205-212
  101. Fukuda, N., Ishii, J., Kaishima, M., Kondo, A. (2011/10) Amplification of agonist stimulation of human G-protein-coupled receptor signaling in yeast, Analytical Biochemistry, 417, 182-187
  102. Matsuda, F., Furusawa, C., Kondo, T., Ishii, J., Shimizu, H., Kondo, A. (2011/09) Engineering strategy of yeast metabolism for higher alcohol production, Microbial Cell Factories, 10: 70
  103. Fukuda, N., Ishii, J., Kondo, A. (2011/09) Gγ recruitment system incorporating a novel signal amplification circuit to screen transient protein-protein interactions, FEBS Journal, 278, 3086-3094
  104. Hasunuma, T., Sanda, T., Yamada, R., Yoshimura, K., Ishii, J., Kondo, A. (2011/01) Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae, Microbial Cell Factories, 10(1): 2
  105. Tanino, T., Hotta, A., Ito, T., Ishii, J., Yamada, R., Hasunuma, T., Ogino, C., Ohmura, N., Ohshima, T., Kondo, A. (2010/11) Construction of a xylose-metabolizing yeast by genome integration of xylose isomerase gene and investigation of the effect of xylitol on fermentation, Applied Microbiology and Biotechnology, 88, 1215-1221
  106. Iguchi, Y., Ishii, J., Nakayama, H., Ishikura, A., Izawa, K., Tanaka, T., Ogino, C., Kondo, A. (2010/06) Control of signalling properties of human somatostatin receptor subtype-5 by additional signal sequences on its amino-terminus in yeast, Journal of Biochemistry, 147(6), 875-884
  107. Togawa, S., Ishii, J., Ishikura, A., Tanaka, T., Ogino, C., Kondo, A. (2010/06) Importance of asparagine residues at positions 13 and 26 on the amino-terminal domain of human somatostatin receptor subtype-5 in signalling, Journal of Biochemistry, 147(6), 867-873
  108. Ishii, J., Fukuda, N., Tanaka, T., Ogino, C., Kondo, A. (Review) (2010/05) Protein-protein interactions and selection: yeast-based approaches that exploit guanine nucleotide-binding protein signaling, FEBS Journal, 277(9), 1982-1995
  109. Fukuda, N., Ishii, J., Tanaka, T., Kondo, A. (2010/04) The competitor-introducedGγ recruitment system, a new approach for screening affinity-enhanced proteins, FEBS Journal, 277(7), 1704-1712
  110. Tanaka, T., Masunari, S., Ishii, J., Wakamura, K., Segawa, M., Fukuda, H., Kondo, A. (2010/01) Displaying non-natural, functional molecules on yeast surfaces via biotin-streptavidin interaction, Journal of Biotechnology, 145, 79-83
  111. Nakamura, Y., Ishii, J., Kondo, A. (2009/11) Split-ubiquitin system for analyzing oligomerization of G protein-coupled receptor, Journal of Bioscience and Bioengineering, 108(1), S36
  112. Ishii, J., Izawa, K., Matsumura, S., Wakamura, K., Tanino T., Tanaka, T., Ogino, C., Fukuda, H., Kondo, A. (2009/06) A simple and immediate method for simultaneously evaluating expression level and plasmid maintenance in yeast, Journal of Biochemistry, 145(6), 701-708
  113. Fukuda, N., Ishii, J., Tanaka, T., Fukuda, H., Kondo, A. (2009/05) Construction of a novel detection system for protein-protein interactions using yeast G-protein signaling, FEBS Journal, 276(9), 2636-2644
  114. Shibasaki, S., Sakata, K., Ishii, J., Kondo, A., Ueda, M. (2008/09) Development of a yeast protein fragment complementation assay (PCA) system using dihydrofolate reductase (DHFR) with specific additives, Applied Microbiology and Biotechnology, 80(4), 735-743
  115. Ishii, J., Tanaka, T., Matsumura, S., Tatematsu, K., Kuroda, S., Ogino, C., Fukuda, H., Kondo, A. (2008/05) Yeast-based fluorescence reporter assay of G protein-coupled receptor signalling for flow cytometric screening: FAR1-disruption recovers loss of episomal plasmid caused by signalling in yeast, Journal of Biochemistry, 143(5), 667-674
  116. Fukuda, N., Ishii, J., Tanaka T., Fukuda, H., Ohnishi, N., Kondo, A. (2008/03) Rapid and efficient selection of yeast displaying a target protein using thermo-responsive magnetic nanoparticles, Biotechnology Progress, 24(2), 352-357
  117. Fukuda, N, Ishii, J., Shibasaki, S, Ueda, M, Fukuda, H, Kondo, A. (2007/08) High-efficiency recovery of target cells using improved yeast display system for detection of protein-protein interactions, Applied Microbiology and Biotechnology, 76(1), 151-158
  118. Shibasaki, S., Kawabata, A., Ishii, J., Yagi, S., Kadonosono, T., Kato, M., Fukuda, N., Kondo, A., Ueda, M. (2007/06) Construction of a novel synergistic system for production and recovery of secreted recombinant proteins by the cell surface engineering, Applied Microbiology and Biotechnology, 75(4), 821-828
  119. Ishii, J., Matsumura, S., Kimura, S., Tatematsu, K., Kuroda, S., Fukuda, H., Kondo, A. (2006/07) Quantitative and dynamic analyses of G protein-coupled receptor signaling yeast using Fus1, enhanced green fluorescence protein (EGFP), and His3 fusion protein, Biotechnology Progress, 22, 954-960

Reviews & Commentaries

  1. 石井 純, バイオものづくりに向けた酵母の発現制御・センシング基盤の開発と応用, 生物工学会誌, 103(3), 104-111 (2025/03)
  2. 冨永将大, 近藤昭彦, 石井純, 酵母における遺伝子スイッチ進化工学ワークフローの「ロバスト化」, 生物物理, 64(3), 144-146 (2024/06)
  3. 伊藤洋一郎, 石井純, 近藤昭彦, ピキア酵母の多重遺伝子欠損による難分泌性抗体タンパク質の生産性向上, Bioscience & Industry, 81(3), 234-236 (2023/05)
  4. 岡橋伸幸, 磯貝章太, 石井純, 松田史生, 出芽酵母代謝工学株が生産するファイトケミカルの高分解能質量分析による構造確認 –プレニルナリンゲニンの分析–, 島津製作所 Application Notes, No.72 (2021/12)
  5. 中村泰之, 近藤昭彦, 石井純, 酵母細胞を用いたG蛋白質共役型受容体リガンドスクリーニングシステムの開発とメタボライトセンサへの応用, Precision Medicine, vol.4, No.13, 60-65 (2021/12)
  6. 中村泰之, 近藤昭彦, 石井純, 酵母細胞を用いたG蛋白質共役型受容体リガンド検出システムの開発とメタボライトセンサへの応用, アグリバイオ, vol.5, No.7, 58-63 (2021/07)
  7. 中村泰之, 近藤昭彦, 石井純, 酵母シグナル伝達経路を利用したリガンド検出システムの開発とメタボライトセンサへの応用, 細胞, 53(5), 37-40 (2021/05)
  8. 柘植謙爾, 石井純, 荒木通啓, 近藤昭彦, ゲノム合成の潮流のインパクト 微生物による物質生産, 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, 36-41 (2018/01)
  9. 中村泰之, 伊藤洋一郎, 梅津光央, 石井純, 近藤昭彦, 低分子抗体医薬の開発展望, バイオインダストリー, Vol.34, No.6, 54-62 (2017/06)
  10. 蓮沼誠久, 石井純, 荻野千秋, 近藤昭彦, バイオリファイナリーの現状と展望, 化学と生物, Vol.53, No.10, 689-695 (2015/10)
  11. 石井純, 荒木通啓, 中津井雅彦, 崎濱由梨, 柘植陽太, 蓮沼誠久, 近藤昭彦, 合成生物工学によるモノづくり微生物のデザインに向けて, 生物工学会誌, 第93巻, 第9号, 523-526 (2015/09)
  12. 石井純, 蓮沼誠久, 松田史生, 近藤昭彦, バイオリファイナリー社会に向けた燃料・化学品生産, 安全工学, Vol.52, No.4, 249-255 (2013/08)
  13. 石井純, 蓮沼誠久, 松田史生, 近藤昭彦, 革新的なものづくり実現のための「合成生物工学」, 生物工学会誌, 91(6), 314-318 (2013/06)
  14. 石井純, GPCRと酵母との出会い, 内藤財団時報, 88, 47 (2011/09)
  15. 石井純, 田中勉, 近藤昭彦, タンパク質間相互作用とシグナル伝達解析, 未来材料, 6, 40-45 (2007/06)
  16. 石井純, 近藤昭彦, コンビナトリアル・バイオエンジニアリングによる新しい創薬システム, 生物工学会誌, 84(8), 319-321 (2006/08)

Books

  1. 戸谷吉博, 松田史生, 石井純, 原清敬, 第1章 バイオものづくりに資する微生物と育種技術 -4. 光をエネルギー源にして利用する有用物質生産大腸菌の開発-, 微生物を活用した有用物質の製造技術, シーエムシー出版, 24-30 (2023/05)
  2. 石井純，新型コロナで変わる時代の実験自動化・遠隔化 「微生物での発酵生産と実験の自動化」, 羊土社，第39巻，第1号，8-12, (2021/01)
  3. Nakamura, Y., Kondo, A., Ishii, J., Biosensing techniques in yeast: G-protein signaling and protein-protein interaction assays for monitoring ligand stimulation and oligomer formation of heterologous GPCRs, Peripheral Membrane Proteins, ISBN 978-1-78923-513-5, IntechOpen, Chapter 3, 25-48 (2018/07)
  4. 石井純, 西晶子, 北野美保, 中村朋美, 庄司信一郎, 秀瀬涼太, 蓮沼誠久, 近藤昭彦, 微生物を用いた物質生産とハイスループット微生物構築技術, スマートセルインダストリー -微生物細胞を用いた物質生産の展望-, 第1編 ハイスループット合成・分析・評価技術, 第2章 ハイスループット微生物構築・評価技術, 39-43, シーエムシー出版 (2018/06)
  5. 化学便覧　応用化学編　28章　バイオマス利用技術
    28.1 近藤昭彦,　28.2.3 荻野千秋,　28.5.1 蓮沼誠久・近藤昭彦,　28.5.3 原清敬・近藤昭彦,　28.6.2 岡井直子・近藤昭彦,　28.6.3 石井純・近藤昭彦,　28.6.6 山田亮祐・近藤昭彦, 丸善出版, 1615-1651 (2014/07)
  6. 石井純, 荻野千秋, 近藤昭彦, 次世代医薬開発に向けた抗体工学の最前線, 第Ⅱ編第４章第4節, 酵母による抗体フラグメントおよび抗体様結合性タンパク質の改変技術, シーエムシー出版, 60-65 (2012/10)
  7. 石井純, 田中勉, 荻野千秋, 近藤昭彦, シングルセル解析の最前線, 第3章4, フローサイトメトリーとＧＦＰレポーターによるＧ蛋白質シグナルのシングルセル解析, シーエムシー出版, 158-165 (2010/03)
  8. 石井純, 近藤昭彦, 第６節 酵母細胞内シグナル定量解析の創薬への応用, 第３章 細胞内生体分子群の動態シグナルの解析，一細胞定量解析の最前線 －ライフサーベイヤ構築に向けて－, シーエムシー出版, 124-134 (2006/12)