Bio-Digital Promotion Office Research Achievements

List of Research Achievements

  1. Arai T*, Wada M, Nishiguchi H, Takimura Y, Ishii J*. (2023) Inducer-free recombinant protein production in Trichoderma reesei: Secretory production of endogenous enzymes and heterologous nanobodies using glucose as the sole carbon source. Microb. Cell Fact. May 19; 22(1): 103
  2. 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) Online SFE-SFC-MS/MS colony screening: A high-throughput approach for optimizing (-)-limonene production. J Chromatogr B Jan 15; 1215: 123588
  3. Morita K, Nishimura Y, Ishii J, Maruyama T. (2022) Micelle-like nanoassemblies of short peptides create antimicrobial selectivity in a conventional antifungal drug. ACS Appl. Nano Mater. Dec 22; 6(2): 1432-1440
  4. Sano M, Tanaka R, Kamata K, Hirono-Hara Y, Ishii J, Matsuda F, Hara KY, Shimizu H, Toya Y. (2022) Conversion of mevalonate to isoprenol using light energy in Escherichia coli without consuming sugars for ATP supply. ACS Synth Biol Dec 16; 11(12): 3966-3972
  5. Otsuka K, Seike T, Toya Y, Ishii J, Hirono-Hara Y, Hara KY, Matsuda F. (2022) Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli. J. Biosci. Bioeng. Dec; 134(6): 484-490
  6. Ito Y, Ishigami M, Hashiba N, Nakamura Y, Terai G, Hasunuma T, Ishii J*, Kondo A*. (2022) Avoiding entry into intracellular protein degradation pathways by signal mutations increases protein secretion in Pichia pastoris. Microb Biotechnol Sep; 15(9): 2364-2378
  7. Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. (2022) Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng Jul; 72: 227-236
  8. Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. (2022) Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng Jul; 72: 227-236
  9. Isogai S, Tominaga M, Kondo A, Ishii J*. (2022) Plant flavonoid production in bacteria and yeasts. Front. Chem. Eng. July 8; 4: 880694 [Review]
  10. Tominaga M, Miyazaki K, Hataya S, Mitsui Y, Kuroda S, Kondo A, Ishii J*. (2022) Enhanced squalene production by modulation of pathways consuming squalene and its precursor. J. Biosci. Bioeng. Jul; 134(1): 1-6
  11. 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) A streamlined strain engineering workflow with genome-wide screening detects enhanced protein secretion in Komagataella phaffii. Commun Biol Jun 8; 5(1): 561
  12. Tominaga M, Kondo A, Ishii J*. (2022) Engineering of synthetic transcriptional switches in yeast. Life Apr 8; 12(4): 557 [Review]
  13. Morita K, Seike T, Ishii J, Matsuda F, Shimizu H. (2022) Improvement of 2,3-butanediol production by dCas9 gene expression system in Saccharomyces cerevisiae. J. Biosci. Bioeng. Mar; 133(3): 208-212
  14. 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) Machine learning discovery of missing links that mediate alternative branches to plant alkaloids. Nat Commun Mar 16; 13(1): 1405
  15. Nishi T, Ito Y, Nakamura Y, Yamaji T, Hashiba N, Tamai M, Yasohara Y, Ishii J*, Kondo A*. (2022) One-step in vivo assembly of multiple DNA fragments and genomic integration in Komagataella phaffii. ACS Synth Biol Feb 18; 11(2): 644-654
  16. Katsurada K, Tominaga M, Kaishima M, Kato H, Matsuno T, Ogino C, Kondo A, Ishii J*, Takayama K. (2021) Constitutive cell surface expression of ZZ domain for the easy preparation of yeast-based immunosorbents. J Gen Appl Microbiol Dec 31; 67(6): 265-268
  17. Yoshida E*, Kojima M, Suzuki M, Matsuda F*, Shimbo K, Onuki A, Nishio Y, Usuda Y, Kondo A, Ishii J*. (2021) Increased carvone production in Escherichia coli by balancing limonene conversion enzyme expression via targeted quantification concatamer proteome analysis. Sci. Rep. Nov 11; 11(1): 22126
  18. Isogai S, Okahashi N, Asama R, Nakamura T, Hasunuma T, Matsuda F, Ishii J*, Kondo A*. (2021) Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases. Metab Eng Commun Jun; 12: e00169.
  19. Shoji S, Yamaji T, Makino H, Ishii J, Kondo A. (2021) Metabolic design for selective production of nicotinamide mononucleotide from glucose and nicotinamide. Metab Eng May; 65: 167-177
  20. Mori Y, Noda S, Shirai T, Kondo A. Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant. (2021) Nat Commun Apr 13; 12(1): 2195
  21. Tominaga M, Nozaki K, Umeno D, Ishii J*, Kondo A. (2021) Robust and flexible platform for directed evolution of yeast genetic switches. Nat Commun Mar 23; 12(1): 1846
  22. Nakamura Y, Asama R, Tabata T, Morita K, Maruyama T, Kondo A, Ishii J*. (2021) Comparative analyses of site-directed mutagenesis of human melatonin MTNR1A and MTNR1B receptors using a yeast fluorescent biosensor. Biotechnol. Bioeng. Feb; 118(2): 863-876
  23. Ito Y, Terai G, Ishigami M, Hashiba N, Nakamura Y, Bamba T, Kumokita R, Hasunuma T, Asai K, Ishii J*, Kondo A*. (2020) Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression. Nucleic Acids Res. Dec 16; 48(22): 13000-13012
  24. Nishimura Y, Ezawa R, Morita K, Nakayama M, Ishii J, Sasaki R, Ogino C, Kondo A. (2020) In vivo evaluation of the ZHER2-BNC/LP carrier encapsulating an anticancer drug and a radiosensitizer. ACS Appl Bio Mater Sep 28; 3(11): 7743–7751
  25. Vavricka CJ, Hasunuma T, Kondo A. (2020) Dynamic metabolomics for engineering biology: Accelerating learning cycles for bioproduction. Trends Biotechnol. Jan; 38(1): 68-82
  26. Morita K, Matsuda F, Okamoto K, Ishii J, Kondo A, Shimizu H. (2019) Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae. Microb. Cell Fact. Oct 15; 18(1): 177
  27. 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) Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids. Nat Commun May 1; 10(1): 2015
  28. Tamano K, Cox RS 3rd, Tsuge K, Miura A, Itoh A, Ishii J, Tamura T, Kondo A, Machida M. (2019) Heterologous production of free dihomo-γ-linolenic acid by Aspergillus oryzae and its extracellular release via surfactant supplementation. J. Biosci. Bioeng. Apr; 127(4): 451-457
  29. Itoh H, Matsui M, Miyamura Y, Takeda I, Ishii J, Kumagai T, Machida M, Shibata T, Arita M. (2018) Biosynthesis of novel statins by combining heterologous genes from Xylaria and Aspergillus. ACS Synth Biol Dec 21; 7(12): 2783-2789
  30. Ito Y, Watanabe T, Aikawa S, Nishi T, Nishiyama T, Nakamura Y, Hasunuma T, Okubo Y, Ishii J*, Kondo A*. (2018) Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in Komagataella phaffii. FEMS Yeast Res. Nov 1; 18(7): foy074
  31. Nakamura Y, Nishi T, Noguchi R, Ito Y, Watanabe T, Nishiyama T, Aikawa S, Hasunuma T, Ishii J*, Okubo Y, Kondo A*. (2018) A stable, autonomously replicating plasmid vector containing Pichia pastoris centromeric DNA. Appl. Environ. Microbiol. Jul 17; 84(15): e02882-17