Publication

【Original Articles】

  1. D. Watanabe*, M. Kumano, Y. Sugimoto, H. Takagi; Spontaneous attenuation of alcoholic fermentation via the dysfunction of Cyc8p in Saccharomyces cerevisiae; Int. J. Mol. Sci. 25(1): 304 (2024)
  2. H. Iwase, Y. Yamamoto, A. Yamada, K. Kawai, S. Oiki, D. Watanabe, B. Mikami, R. Takase, W. Hashimoto*; Crystal structures of Lacticaseibacillus 4-deoxy-L-threo-5-hexosuloseuronate ketol-isomerase KduI in complex with substrate analogs; J. Appl. Glycosci. 70(4): 99-107 (2023)
  3. D. Watanabe*, M. Kawashima, N. Yoshioka, Y. Sugimoto, H. Takagi; Rational design of alcoholic fermentation targeting extracellular carbon; NPJ Sci. Food 7(1): 37 (2023)
  4. D. Watanabe, W. Hashimoto*; Adaptation of yeast Saccharomyces cerevisiae to grape-skin environment; Sci. Rep. 13: 9279 (2023)
  5. K. Anamizu, R. Takase, M. Hio, D. Watanabe, B. Mikami, W. Hashimoto*; Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation; Sci. Rep. 12: 12653 (2022)
  6. S. Yabuuchi, S. Oiki, S. Minami, R. Takase, D. Watanabe, W. Hashimoto*; Enhanced propagation of Granulicatella adiacens from human oral microbiota by hyaluronan; Sci. Rep. 12: 10948 (2022)
  7. S. Nakatsuji, K. Okumura, R. Takase, D. Watanabe, B. Mikami, and W. Hashimoto*; Crystal structures of EfeB and EfeO in a bacterial siderophore-independent iron transport system; Biochem. Biophys. Res. Commun. 594: 124-130 (2022)
  8. T. Chadani, S. Ohnuki, A. Isogai, T. Goshima, M. Kashima, F. Ghanegolmohammadi, T. Nishi, D. Hirata, D. Watanabe, K. Kitamoto, T. Akao, and Y. Ohya*; Genome editing to generate sake yeast strains with eight mutations that confer excellent brewing characteristics; Cells 10(6): 1299 (2021)
  9. T. Murakami, M. Watanabe, M. Takaki, H. Suetsugu-Sasaki, D. Watanabe, T. Goshima, H. Fukuda, H. Shimoi, and T. Akao*; Isolation of novel alcohol-tolerant spontaneous mutant strains from sake yeast Kyokai no. 6 and no. 7, and their brewing characteristics; J. Brew. Soc. Japan 116(2): 131-141 (2021) [Japanese]
  10. R. Tanahashi, T. S. N. Afiah, A. Nishimura, D. Watanabe, and H. Takagi*; The C2 domain of the ubiquitin ligase Rsp5 is required for ubiquitination of the endocytic protein Rvs167 upon change of nitrogen source; FEMS Yeast Res. 20(7): foaa058 (2020)
  11. H. Sugiura, A. Nagase, S. Oiki, B. Mikami, D. Watanabe, and W. Hashimoto*; Bacterial inducible expression of plant cell wall-binding protein YesO through conflict between Glycine max and saprophytic Bacillus subtilis; Sci. Rep. 10(1): 18691 (2020)
  12. M. Kanai*, T. Kawata, T. Morimoto, M. Mizunuma, D. Watanabe, T. Akao, T. Fujii, and H. Iefuji; The sake yeast YHR032W/ERC1 allele contributes to the regulation of the tetrahydrofolate content in the folate synthetic pathway in sake yeast strains; Biosci. Biotechnol. Biochem. 84(5): 1073-1076 (2020)
  13. S. Nakata, M. Hio, R. Takase, S. Kawai, D. Watanabe, and W. Hashimoto*; Polyunsaturated fatty acids-enriched lipid from reduced sugar alcohol mannitol by marine yeast Rhodosporidiobolus fluvialis Y2; Biochem. Biophys. Res. Commun. 526(4): 1138-1142 (2020)
  14. N. S. B. Mat Nanyan, D. Watanabe, Y. Sugimoto, and H. Takagi*; Effect of the deubiquitination enzyme gene UBP6 on the stress-responsive transcription factor Msn2-mediated control of the amino acid permease Gnp1 in yeast. J. Biosci. Bioeng. 129(4): 423-427 (2020)
  15. Y. Mukai*, Y. Kamei, X. Liu, S. Jiang, Y. Sugimoto, N. S. B. Mat Nanyan, D. Watanabe, and H. Takagi*; Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae; Microb. Cell 6(10): 482-490 (2019)
  16. N. S. B. Mat Nanyan†, D. Watanabe†, Y. Sugimoto, and H. Takagi*; Involvement of the stress-responsive transcription factor gene MSN2 in the control of amino acid uptake in Saccharomyces cerevisiae; FEMS Yeast Res.19(5): foz052 (2019) [†equally contributed]
  17. D. Watanabe, S. Tashiro, D. Shintani, Y. Sugimoto, A. Iwami, Y. Kajiwara, H. Takashita, and H. Takagi*; Loss of Rim15p in shochu yeast alters carbon utilization during barley shochu fermentation; Biosci. Biotechnol. Biochem. 83(8): 1594-1597 (2019)
  18. M. Ohashi, R. Nasuno, D. Watanabe, and H. Takagi*; Stable N-acetyltransferase Mpr1 improves ethanol productivity in the sake yeast Saccharomyces cerevisiae; J. Ind. Microbiol. Biotechnol. 46(7): 1039-1045 (2019)
  19. T. Abe, Y. Toyokawa, Y. Sugimoto, H. Azuma, K. Tsukahara, R. Nasuno, D. Watanabe, M. Tsukahara*, and H. Takagi*; Characterization of a new Saccharomyces cerevisiae isolated from hibiscus flower and its mutant with l-leucine accumulation for awamori brewing; Front. Genet. 10: 490 (2019)
  20. H. Shimoi*, Y. Hanazumi, N. Kawamura, M. Yamada, S. Shimizu, T. Suzuki, D. Watanabe, and T. Akao; Meiotic chromosomal recombination defect in sake yeasts; J. Biosci. Bioeng. 127(2): 190-196 (2019)
  21. D. Watanabe*, T. Kajihara, Y. Sugimoto, K. Takagi, M. Mizuno, Y. Zhou, J. Chen, K. Takeda, H. Tatebe, K. Shiozaki, N. Nakazawa, S. Izawa, T. Akao, H. Shimoi, T. Maeda, and H. Takagi; Nutrient signaling via the TORC1-Greatwall-PP2AB55δ pathway is responsible for the high initial rates of alcoholic fermentation in sake yeast strains of Saccharomyces cerevisiae; Appl. Environ. Microbiol. 85(1): e02083-18 (2019)
  22. M. Oomuro*, D. Watanabe, Y. Sugimoto, T. Kato, Y. Motoyama, T. Watanabe, and H. Takagi; Accumulation of intracellular S-adenosylmethionine increases the fermentation rate of bottom-fermenting brewer’s yeast during high-gravity brewing; J. Biosci. Bioeng. 126(6): 736-741 (2018)
  23. D. Watanabe*, M. Kumano, Y. Sugimoto, M. Ito, M. Ohashi, K. Sunada, T. Takahashi, T. Yamada, and H. Takagi; Metabolic switching of sake yeast by kimoto lactic acid bacteria through the [GAR+] non-genetic element; J. Biosci. Bioeng. 126(5): 624-629 (2018)
  24. T. Akao*, Y. Zhou, D. Watanabe, N. Okazaki, and H. Shimoi; Development of DNA markers to differentiate good Kyokai sake yeast and other yeast strains; J. Brew. Soc. Japan 113(10): 631-641 (2018) [Japanese]
  25. D. Watanabe, H. Sekiguchi, Y. Sugimoto, A. Nagasawa, N. Kida, and H. Takagi*; Importance of proteasome gene expression during model dough fermentation after preservation of baker’s yeast cells by freezing; Appl. Environ. Microbiol. 84(12): e00406-18 (2018)
  26. N. Takpho, D. Watanabe, and H. Takagi*; Valine biosynthesis in Saccharomyces cerevisiae is regulated by the mitochondrial branched-chain amino acid aminotransferase Bat1; Microb. Cell 5(6): 293-299 (2018)
  27. N. Takpho, D. Watanabe, and H. Takagi*; High-level production of valine by expression of the feedback inhibition-insensitive acetohydroxyacid synthase in Saccharomyces cerevisiae; Metab. Eng. 46: 60-67 (2018)
  28. A. Watcharawipas, D. Watanabe, and H. Takagi*; Enhanced sodium acetate tolerance in Saccharomyces cerevisiae by the Thr255Ala mutation of the ubiquitin ligase Rsp5; FEMS Yeast Res. 17(8): fox083 (2017)
  29. S. Ohnuki, H. Okada, A. Friedrich, Y. Kanno, T. Goshima, H. Hasuda, M. Inahashi, N. Okazaki, H. Tamura, R. Nakamura, D. Hirata, H. Fukuda, H. Shimoi, K. Kitamoto, D. Watanabe, J. Schacherer, T. Akao*, and Y. Ohya*; Phenotypic diagnosis of lineage and differentiation during sake yeast breeding; G3: Genes Genom. Genet. 7(8): 2807-2820 (2017)
  30. D. Watanabe, A. Kaneko, Y. Sugimoto, S. Ohnuki, H. Takagi, and Y. Ohya*; Promoter engineering of the Saccharomyces cerevisiae RIM15 gene for improvement of alcoholic fermentation rates under stress conditions; J. Biosci. Bioeng. 123(2): 183-189 (2017)
  31. M. Kanai*, T. Kawata, Y. Yoshida, Y. Kita, T. Ogawa, M. Mizunuma, D. Watanabe, H. Shimoi, A. Mizuno, O. Yamada, T. Fujii, and H. Iefuji; Sake yeast YHR032W/ERC1 haplotype contributes to high S-adenosylmethionine accumulation in sake yeast strains; J. Biosci. Bioeng. 123(1): 8-14 (2017)
  32. A. Tsolmonbaatar, K. Hashida, Y. Sugimoto, D. Watanabe, S. Furukawa, and H. Takagi*; Isolation of baker’s yeast mutants with proline accumulation that showed enhanced tolerance to baking-associated stresses; Int. J. Food Microbiol. 238: 233-240 (2016)
  33. M. Oomuro*, T. Kato, Y. Zhou, D. Watanabe, Y. Motoyama, H. Yamagishi, T. Akao, and M. Aizawa; Defective quiescence entry promotes the fermentation performance of bottom-fermenting brewer’s yeast; J. Biosci. Bioeng. 122(5): 577-582 (2016)
  34. I. Nishida, D. Watanabe, and H. Takagi*; Putative mitochondrial α-ketoglutarate- dependent dioxygenase Fmp12 controls utilization of proline as an energy source in Saccharomyces cerevisiae; Microb. Cell 3(10): 522-528 (2016)
  35. Y. Tatehashi, D. Watanabe, and H. Takagi*; γ-Glutamyl kinase is involved in selective autophagy of ribosomes in Saccharomyces cerevisiae; FEBS Lett. 590(17): 2906-2914 (2016)
  36. I. Nishida†, D. Watanabe†, A. Tsolmonbaatar, T. Kaino, I. Ohtsu, and H. Takagi*; Vacuolar amino acid transporters upregulated by exogenous proline and involved in cellular localization of proline in Saccharomyces cerevisiae. J. Gen. Appl. Microbiol. 62(3): 132-139 (2016) [†equally contributed]
  37. Y. Yoshikawa, R. Nasuno, N. Kawahara, A. Nishimura, D. Watanabe, and H. Takagi*; Regulatory mechanism of the flavoprotein Tah18-dependent nitric oxide synthesis and cell death in yeast. Nitric Oxide 57: 85-91 (2016)
  38. R. Nasuno, S. Hirase, S. Norifune, D. Watanabe, and H. Takagi*; Structure-based molecular design for thermostabilization of N-acetyltransferase Mpr1 involved in a novel pathway of l-arginine synthesis in yeast; J. Biochem. 159(2): 271-277 (2016)
  39. R. I. Astuti†, D. Watanabe†, and H. Takagi*; Nitric oxide signaling and its role in oxidative stress response in Schizosaccharomyces pombe. Nitric Oxide52: 29-40 (2016) [†equally contributed]
  40. D. Watanabe, Y. Zhou, A. Hirata, Y. Sugimoto, K. Takagi, T. Akao, Y. Ohya, H. Takagi, and H. Shimoi*; Inhibitory role of Greatwall-like protein kinase Rim15p in alcoholic fermentation via upregulating the UDP-glucose synthesis pathway in Saccharomyces cerevisiae; Appl. Environ. Microbiol. 82(1): 340-351 (2016)
  41. E. Funahashi, K. Saiki, K. Honda, Y. Sugiura, Y. Kawano, I. Ohtsu*, D. Watanabe, Y. Wakabayashi, T. Abe, T. Nakanishi, M. Suematsu, and H. Takagi; Finding of thiosulfate pathway for synthesis of organic sulfur compounds in Saccharomyces cerevisiae and improvement of ethanol production; J. Biosci. Bioeng. 120(6): 666-669 (2015)
  42. D. Watanabe, H. Murai, R. Tanahashi, K. Nakamura, T. Sasaki, and H. Takagi*; Cooperative and selective roles of the WW domains of the yeast Nedd4-like ubiquitin ligase Rsp5 in the recognition of the arrestin-like adaptors Bul1 and Bul2; Biochem. Biophys. Res. Commun. 463(1-2): 76-81 (2015)
  43. S. Hirayama, M. Shimizu, N. Tsuchiya, S. Furukawa, D. Watanabe, H. Shimoi, H. Takagi, H. Ogihara, and Y. Morinaga*; Awa1p on the cell surface of sake yeast inhibits biofilm formation and the co-aggregation between sake yeasts and Lactobacillus plantarum ML11-11; J. Biosci. Bioeng. 119(5): 532-537 (2015)
  44. I. Wijayanti†, D. Watanabe†, S. Oshiro, and H. Takagi*; Isolation and functional analysis of yeast ubiquitin ligase Rsp5 variants that alleviate the toxicity of human α-synuclein; J. Biochem.157(4): 251-260 (2015) [†equally contributed]
  45. H. Takagi*, K. Hashida, D. Watanabe, R. Nasuno, M. Ohashi, T. Iha, M. Nezuo, and M. Tsukahara; Isolation and characterization of awamori yeast mutants with l-leucine accumulation that overproduce isoamyl alcohol; J. Biosci. Bioeng. 119(2): 140-147 (2015)
  46. K. Uehara*, J. Watanabe, T. Akao, D. Watanabe, Y. Mogi, and H. Shimoi; Screening of high-level 4-hydroxy-2 (or 5)-ethyl-5 (or 2)-methyl-3(2H)-furanone-producing strains from a collection of gene deletion mutants of Saccharomyces cerevisiae; Appl. Environ. Microbiol. 81(1): 453-460 (2015)
  47. T. Shiga, N. Yoshida, Y. Shimizu, E. Suzuki, T. Sasaki, D. Watanabe, and H. Takagi*; Quality control of plasma membrane proteins by Saccharomyces cerevisiae Nedd4-like ubiquitin ligase Rsp5p under environmental stress conditions; Eukaryot. Cell 13(9): 1191-1199 (2014)
  48. D. Watanabe, R. Kikushima, M. Aitoku, A. Nishimura, I. Ohtsu, R. Nasuno, and H. Takagi*; Exogenous addition of histidine reduces copper availability in the yeast Saccharomyces cerevisiae; Microb. Cell 1(7): 241-246 (2014)
  49. S. Uesugi, D. Watanabe, M. Kitajima, R. Watanabe, Y. Kawamura, M. Ohnishi, H. Takagi, and K. Kimura*; Calcineurin inhibitors suppress the high-temperature stress sensitivity of the yeast ubiquitin ligase Rsp5 mutant: a new method of screening for calcineurin inhibitors; FEMS Yeast Res. 14(4): 567-574 (2014)
  50. T. Inaba, D. Watanabe, Y. Yoshiyama, K. Tanaka, J. Ogawa, H. Takagi, H. Shimoi, and J. Shima*; An organic acid-tolerant HAA1-overexpression mutant of an industrial bioethanol strain of Saccharomyces cerevisiae and its application to the production of bioethanol from sugarcane molasses; AMB Express 3(1): 74 (2013)
  51. D. Watanabe, N. Hashimoto, M. Mizuno, Y. Zhou, T. Akao, and H. Shimoi*; Accelerated alcoholic fermentation caused by defective gene expression related to glucose derepression in Saccharomyces cerevisiae; Biosci. Biotechnol. Biochem. 77(11): 2255-2262 (2013)
  52. T. Inai†, D. Watanabe†, Y. Zhou, R. Fukada, T. Akao, J. Shima, H. Takagi, and H. Shimoi*; Rim15p-mediated regulation of sucrose utilization during molasses fermentation using Saccharomyces cerevisiae strain PE-2; J. Biosci. Bioeng.116(5): 591-594 (2013) [†equally contributed]
  53. K. Wakabayashi, A. Isogai*, D. Watanabe, A. Fujita, and S. Sudo; Involvement of methionine salvage pathway genes of Saccharomyces cerevisiae in the production of precursor compounds of dimethyl trisulfide (DMTS); J. Biosci. Bioeng. 116(4): 475-479 (2013)
  54. D. Watanabe, Y. Araki, Y. Zhou, N. Maeya, T. Akao, and H. Shimoi*; A loss-of-function mutation in the PAS kinase Rim15p is related to defective quiescence entry and high fermentation rates in Saccharomyces cerevisiae sake yeast strains; Appl. Environ. Microbiol. 78(11): 4008-4016 (2013)
  55. Y. Sasano†, D. Watanabe†, K. Ukibe, T. Inai, I. Ohtsu, H. Shimoi, and H. Takagi*; Overexpression of the yeast transcription activator Msn2 confers furfural resistance and increases the initial fermentation rate in ethanol production; J. Biosci. Bioeng. 113(4): 451-455 (2012) [†equally contributed]
  56. C. Noguchi†, D. Watanabe†, Y. Zhou, T. Akao, and H. Shimoi*; Association of constitutive hyperphosphorylation of Hsf1p with a defective ethanol stress response in Saccharomyces cerevisiae sake yeast strains; Appl. Environ. Microbiol.78(2): 385-392 (2012) [†equally contributed]
  57. D. Watanabe, S. Nogami, Y. Ohya, Y. Kanno, Y. Zhou, T. Akao, and H. Shimoi*; Ethanol fermentation driven by elevated expression of the G1 cyclin gene CLN3 in sake yeast; J. Biosci. Bioeng. 112(6): 577-582 (2011)
  58. T. Akao, I. Yashiro, A. Hosoyama, H. Kitagaki, H. Horikawa, D. Watanabe, R. Akada, Y. Ando, S. Harashima, T. Inoue, Y. Inoue, S. Kajiwara, K. Kitamoto, N. Kitamoto, O. Kobayashi, S. Kuhara, T. Masubuchi, H. Mizoguchi, Y. Nakao, A. Nakazato, M. Namise, T. Oba, T. Ogata, A. Ohta, M. Sato, S. Shibasaki, Y. Takatsume, S. Tanimoto, H. Tsuboi, A. Nishimura, K. Yoda, T. Ishikawa, K. Iwashita, N. Fujita, and H. Shimoi*; Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7; DNA Res. 18(6): 423-434 (2011)
  59. D. Watanabe, T. Ota, F. Nitta, T. Akao, and H. Shimoi*; Automatic measurement of sake fermentation kinetics using a multi-channel gas monitor system; J. Biosci. Bioeng. 112(1): 54-57 (2011)
  60. H. Urbanczyk, C. Noguchi, H. Wu, D. Watanabe, T. Akao, H. Takagi, and H. Shimoi*; Sake yeast strains have difficulty in entering a quiescent state after cell growth cessation; J. Biosci. Bioeng. 112(1): 44-48 (2011)
  61. D. Watanabe, H. Wu, C. Noguchi, Y. Zhou, T. Akao, and H. Shimoi*; Enhancement of the initial rate of ethanol fermentation due to dysfunction of yeast stress response components Msn2p and/or Msn4p; Appl. Environ. Microbiol. 77(3): 934-941 (2011)
  62. M. Watanabe, D. Watanabe, S. Nogami, S. Morishita, and Y. Ohya*; Comprehensive and quantitative analysis of yeast deletion mutants defective in apical and isotropic bud growth; Curr. Genet. 55(4): 365-380 (2009)
  63. M. Watanabe, D. Watanabe, T. Akao, and H. Shimoi*; Overexpression of MSN2 in a sake yeast strain promotes ethanol tolerance and increases ethanol production in sake brewing; J. Biosci. Bioeng. 107(5): 516-518 (2009)
  64. M. Suzuki, Y. Asada, D. Watanabe, and Y. Ohya*; Cell shape and growth of budding yeast cells in restrictive microenvironments; Yeast 21(12): 983-989 (2004)
  65. T. L. Saito*, M. Ohtani, H. Sawai, F. Sano, A. Saka, D. Watanabe, M. Yukawa, Y. Ohya, and S. Morishita; SCMD: Saccharomyces cerevisiae morphological database; Nucleic Acids Res. 32(Database issue): D319-D322 (2004)
  66. M. Sekiya-Kawasaki, M. Abe, A. Saka, D. Watanabe, K. Kono, M. Minemura-Asakawa, S. Ishihara, T. Watanabe, and Y. Ohya*; Dissection of upstream regulatory components of the Rho1p effector, 1,3-β-glucan synthase, in Saccharomyces cerevisiae; Genetics 162(2): 663-676 (2002)
  67. T. Utsugi, M. Minemura, A. Hirata, M. Abe, D. Watanabe, and Y. Ohya*; Movement of yeast 1,3-β-glucan synthase is essential for uniform cell wall synthesis; Genes Cells 7(1): 1-9 (2002)
  68. D. Watanabe, M. Abe, and Y. Ohya*; Yeast Lrg1p acts as a specialized RhoGAP regulating 1,3-β-glucan synthesis; Yeast 18(10): 943-951 (2001)

【Review Articles】(English only)

  1. D. Watanabe; Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation; Biosci. Biotechnol. Biochem. 88: 237-241 (2024)
  2. D. Watanabe and H. Takagi; Yeast prion-based metabolic reprogramming induced by bacteria in fermented foods; FEMS Yeast Res. 19: foz061 (2019)
  3. A. Watcharawipas, D. Watanabe, and H. Takagi; Sodium acetate tolerance in Saccharomyces cerevisiae and the ubiquitin ligase Rsp5; Front. Microbiol. 9: 2495 (2018)
  4. D. Watanabe and H. Takagi; Pleiotropic functions of the yeast Greatwall-family protein kinase Rim15p: a novel target for the control of alcoholic fermentation; Biosci. Biotech. Biochem. 81: 1061-1068 (2017)
  5. D. Watanabe, H. Takagi, and H. Shimoi; Mechanism of High Alcoholic Fermentation Ability of Sake Yeast; ”Stress Biology of Yeasts and Fungi: Applications for Industrial Brewing and Fermentation” H. Takagi and H. Kitagaki (eds.) p.59-75, Springer (2015)