論文発表

2018年4月より「蛋白質化学工学分野」と「生物化学分野」が統合し、一つの研究室として新たに「生物化学分野」がスタートしました。
リンクで2017年までのページを表示します。

2022年

  • Matsumoto, S., Ono, S., Shinoda, S., Kakuta, K., Okada, S., Ito, T., Numata, T., and Endo, T. (2022) GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER. J. Cell Biol. 221: in press
  • Nagai, S., Sildever, S., Nishi, N., Tazawa, S., Basti, L., Kobayashi, T., and Ishino, Y. (2022) Comparing PCR-generated artifacts of different polymerases for improved accuracy of DNA metabarcoding. Metabarcoding and Metagenomics 6: 27–39. doi: 10.3897/mbmg.6.77704
  • Yaeshima, C., Murata, N., Ishino, S., Sagawa, I., Ito, K., and Uchiumi, T. (2022) A novel ribosome-dimerization protein found in the hyperthermophilic archaeon Pyrococcus furiosus using ribosome-associated proteomics. Biochem. Biophys. Res. Commun. 593, 116-121. doi: 10.1016/j.bbrc.2022.01.043.
  • Suzuki, S., Kurosawa, N., Yamagami, T., Matsumoto, S., Numata, T., Ishino, S., and Ishino, Y. (2022) Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Catalysts 12: 34. doi: 10.3390/catal12010034
  • Feng, X., Zhang, B., Xu, R., Gao, Z., Liu, X., Yuan, G., Ishino, S., Feng, M., Shen, Y., Ishino, Y. and She, Q. (2022) A well conserved archaeal B-family polymerase functions as a mismatch and lesion extender. mBio 13(1):e0265921. doi: 10.1128/mbio.02659-21.
  • Fujikane, A., Sakamoto, A., Fujikane, R., Nishi, A., Ishino, Y., Hiromatsu, K., and Nabeshima, S. (2022) Inhibition of respiratory syncytial virus infectivity by Ephedrae Herba and 1 Cinnamomi Cortex through interaction with G glycoprotein. Comm Biol. 5: 94. doi: 10.1038/s42003-022-03046-z.

2021年

  • Feng, X., Zhang, B., Xu, R., Gao, Z., Liu, X., Yuan, G., Ishino, S., Feng, M., Shen, Y., Ishino, Y. and She, Q. (2021) Enzymatic switching between archaeal DNA polymerases facilitates abasic site bypass. Frontier Microbiol. 12: 802670. doi: 10.3389/fmicb.2021.802670.
  • Matsumoto, K., Sakami, T., Watanabe, T., Taniuchi, Y., Kuwata, A., Kakehi, S., Engkong, T., Igarashi, Y., Kinoshita, S., Asakawa, S., Hattori, M., Watabe, S., Ishino, Y., Kobayashi, T., Ikeo, K., and Gojobori, T. (2021) Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters. PLoS ONE, 16 e0257862. doi: 10.1371/journal.pone.0257862
  • Oki, K., Nagata, M., Yamagami, T., Numata, T., Ishino, S., Oyama, O., and Ishino, Y. (2021) Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. Nucleic Acids Res. 49, gkab799. https://doi.org/10.1093/nar/gkab799 (Selected as Breakthrough Article of NAR).
  • Balaratnam, S., Rhodes, C., Bume, D.D., Connelly, C., Lai, C.C., Kelley, J.A., Yazdani, K., Homan, P.J., Incarnato, D., Numata, T., and Schneekloth, J.S. (2021) A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites. Nat. Comm. 12, Article number: 5856
  • Teramoto, T., Koyasu, T., Adachi, N., Kawasaki, M., Moriya, T., Numata, T., Senda, T. and Kakuta, Y. (2021) Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis. J. Biol. Chem. 297, 3, 101028.
  • Medvedeva, S., Brandt, D., Cvirkaite-Krupovic, V., Liu, Y., Severinov, K., Ishino, S., Ishino, Y., Prangishvili, D., Kalinowski, J., and Krupovic, M. (2021) New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae. Environ Microbiol. 23: 4612-4630. doi:10.1111/1462-2920.15654
  • Yoshitake, K., Kimura, G., Sakami, T., Watanabe, T., Taniuchi, Y., Kakehi, S., Kuwata, A., Yamaguchi, H., Kataoka, T., Kawachi, M., Ikeo, K., Tan, E., Igarashi, Y., Ohtsubo, M., Watabe, S., Suzuki, Y., Asakawa, S., Ishino, S., Tashiro, K., Ishino, Y., Kobayashi, T., Mineta, K., and Gojobori, T. (2021) Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Sci. Rep. 11: 12222. https://doi.org/10.1038/s41598-021-91615-3
  • Oki, K., Yamagami, T., Nagata, M., Mayanagi, K., Shirai T., Adachi, N., Numata, T., Ishino, S., and Ishino, Y. (2021) DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen. Nucleic Acids Res. 49: 4599-4612 doi:10.1093/nar/gkab243

2020年

  • Mayanagi, K., Oki, K., Miyazaki, N., Ishino, S., Yamagami, T., Morikawa, K., Iwasaki, K., Kohda, D., Shirai, T., and Ishino, Y. (2020) Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. BMC Biol. 18: 152. doi: 10.1186/s12915-020-00889-y
  • Koonin, E.V., Krupovic, M., Ishino, S., and Ishino, Y. (2020) The replication machinery of LUCA: common origin of DNA replication and transcription. BMC Biol. 18: 61. doi: 10.1186/s12915-020-00800-9
  • Hogrel, G., Lu, Y., Alexandre, N., Bossé, A., Dulermo, R., Ishino, S., Ishino, Y., and Flament, D. (2020) Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea. Biomolecules 10: 1045. doi: 10.3390/biom10071045.
  • Ishino, Y. (2020) Studies on DNA-related enzymes to elucidate molecular mechanisms underlying genetic information processing and their application in genetic engineering. Biosci Biotechnol Biochem. 1-18. (AWARD REVIEW) doi: 10.1080/09168451.2020.1778441

2019年

  • Takeshita, D., Sato, M., Inanaga, H., and Numata, T. (2019) Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex. J. Mol. Biol. 431: 748-763. doi: 10.1016/j.jmb.2019.01.009.
  • Matsumoto, S., Nakatsukasa, K., Kakuta, C., Tamura, Y., Esaki, M., and Endo, T. (2019) Msp1 Clears Mistargeted Proteins by Facilitating Their Transfer from Mitochondria to the ER. Molecular Cell. 76: 191-205.
  • Ueda, E., Tamura, Y., Sakaue, H., Kawano, S., Kakuta, C., Matsumoto, S., and Endo, T. (2019) Myristoyl group-aided protein import into the mitochondrial intermembrane space. Sci. Rep. 9: 1185. doi: 10.1038/s41598-018-38016-1.
  • Takashima, T., Taku, T., Yamanaka, T., Fukamizo, T., Numata, T., and Ohnuma, T. (2019) Crystal structure and biochemical characterization of CJP38, a β-1,3-glucanase and allergen of Cryptomeria japonica pollen. Mol. Immunol. 116:199-207. doi: 10.1016/j.molimm.2019.10.016.
  • Maruyama, K., Imai, H., Kawamura, M., Ishino, S., Ishino, Y., Ito, K., and Uchiumi, T. (2019) Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations. Sci Rep. 9:14761. doi: 10.1038/s41598-019-51266-x.
  • Kushida, T., Narumi, I., Ishino, S., Ishino, Y., Fujiwara, S., Imanaka, T., and Higashibata, H. (2019). PolB, a Family B DNA Polymerase, in Thermococcus kodakarensis is important for DNA repair, but not DNA Replication. Microbes Environ. 34, 316-326. doi: 10.1264/jsme2.ME19075. Epub 2019 Jul 27.
  • Igarashi, Y., Mori, D., Mitsuyama, S., Yoshitake, K., Ono, H., Watanabe, T., Taniuchi, Y., Sakami, T., Kuwata, A., Kobayashi, T., Ishino, Y., Watabe, S., Gojobori, T., and Asakawa, S. (2019). A preliminary metagenome analysis based on a combination of protein domains. Proteomes, 7(2). pii: E19. doi: 10.3390/proteomes7020019.
  • Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H., Sinniah, R.S., Barchi, J.J., Ferré-D'Amaré, A.R., and Schneekloth, J.S. Jr. (2019) Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure. Nat. Commun. 10: 1501. doi:10.1038/s41467-019-09493-3.

2018年

  • Nagata, M., Ishino, S., Yamagami, T., and Ishino, Y. (2018) Replication protein A complex in Thermococcus kodakarensis interacts with DNA polymerases and helps their effective strand synthesis. Biosci. Biotechnol. Biochem. 83: 695-704 doi: 10.1080/09168451.2018.1559722. Epub 2018Dec22.
  • Takashima, N., Ishino, S., Oki, K., Takafuji, M., Yamagami, T., Matsuo, R., Mayanagi, K., and Ishino, Y. (2018) Elucidating functions of DP1 and DP2 subunits from the Thermococcus kodakarensis family D DNA polymerase. Extremophiles 23: 161–172 doi: 10.1007/s00792-018-1070-3.
  • Liu, Y., Brandt, D., Ishino, S., Ishino, Y., Koonin, E.V., Kalinowski, J., Krupovic, M., and Prangishvili, D. (2018) New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures. Environ. Microbiol. doi: 10.1111/1462-2920.14479.
  • Mayanagi, K., Ishino, S., Shirai, T., Oyama, T., Kiyonari, S., Kohda, D., Morikawa, K., and Ishino, Y. (2018) Direct visualization of DNA baton pass between replication factors bound to PCNA. Sci. Rep. 8:16209. doi: 10.1038/s41598-018-34176-2.
  • Shiraishi, M., Ishino, S., Heffernan, M., Cann, I., and Ishino, Y. (2018) The mesophilic archaeon Methanosarcina acetivorans counteracts uracil in DNA with multiple enzymes: EndoQ, ExoIII, and UDG. Sci Rep. 8, 1-14. doi: 10.1038/s41598-018-34000-x
  • Ishino, S., Skouloubris, S., Kudo, H., l'Hermitte-Stead, C., Es-Sadik, A., Lambry, J.C., Ishino, Y., and Myllykallio, H. (2018) Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication. Nucleic Acids Res. 46, 6206-6217. doi: 10.1093/nar/gky460.
  • 石野良純 (2018) CRISPR発見から30年(巻頭言)化学と生物 56, 237.
  • Miyazono, K.I., Ishino, S., Makita, N., Ito, T., Ishino, Y., and Tanokura, M. (2018) Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus.  Nucleic Acids Res. 45, 4807-4818. doi: 10.1093/nar/gky261.
  • Daimon, K., Ishino, S., Imai, N., Nagumo, S., Yamagami, T., Matsukawa, H. and Ishino, Y. (2018) Two Family B DNA Polymerases From Aeropyrum pernix, Based on Revised Translational Frames. Frontiers in Molecular Biosciences 5. doi: 10.3389/fmolb.2018.00037. eCollection 2018
  • Ishino, Y., Krupovic, M., and Forterre, P. (2018) History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology. J. Bacteriol. 200: pii: e00580-17. doi: 10.1128/JB.00580-17.
  • Oshima, K., Gao, X., Hayashi, S., Ueda, T., Nakashima, T., and Kimura, M. (2018) Crystal structure of an archaeal ribonuclease P protein Rpp38 in complex with RNA fragments containing a K-turn motif. Acta Cryst. F74, 57-64

生物化学研究室(2017年まで)

蛋白質化学工学研究室(2017年まで)

  • 農学研究院 生命機能科学部門 生物機能分子化学講座 生物化学分野
  • 生物資源環境科学府 生命機能科学専攻 生物機能分子化学コース 生物化学分野
  • 農学部 応用生物科学コース 応用生命化学分野 生物化学研究室
  • Biological Chemistry, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences
  • システム生命科学府 生命工学講座 極限環境生物工学研究室
  • Biotechnology of Extremophiles, Division of Life Engineering, Graduate School of Systems Life Sciences
Copyright © Yoshizumi Ishino, All Rights Reserved.