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。
2024年
- Parmar S, Bume DD, Connelly CM, Boer RE, Prestwood PR, Wang Z, Labuhn H, Sinnadurai K, Feri A, Ouellet J, Homan P, Numata T, Schneekloth JS Jr. (2024) Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression. Nat. Commun. 15:8173. doi: 10.1038/s41467-024-52235-3.
- Tanaka S, Elgaabari A, Seki M, Kuwakado S, Zushi K, Miyamoto J, Sawano S, Mizunoya W, Ehara K, Watanabe N, Ogawa Y, Imakyure H, Fujimaru R, Osaki R, Shitamitsu K, Mizoguchi K, Ushijima T, Maeno T, Nakashima T, Suzuki T, Nakamura M, Anderson JE, Tatsumi R. (2024) In vitro immuno-prevention of nitration/dysfunction of myogenic stem cell activator HGF, towards developing a strategy for age-related muscle atrophy. Aging Cell. 23:e14337. doi: 10.1111/acel.14337.
- Matsumoto S, Ono S, Endo T(2024) Analysis of protein trafficking between mitochondria and the endoplasmic reticulum by fluorescence microscopy. Methods Enzymol. In press. doi: 10.1016/bs.mie.2024.07.041.
2023年
- Elgaabari A, Imatomi N, Kido H, Nakashima T, Okuda S, Manabe Y, Sawano S, Mizunoya W, Kaneko R, Tanaka S, Maeno T, Matsuyoshi Y, Seki M, Kuwakado S, Zushi K, Daneshvar N, Nakamura M, Suzuki T, Sunagawa K, Anderson JE, Allen RE, Tatsumi R. (2024) Age-related nitration/dysfunction of myogenic stem cell activator HGF. Aging Cell 23:e14041 doi:10.1111/acel.14041
- Matsumoto S. (2023) Msp1-mediated proofreading mechanism for localization of tail-anchored membrane proteins. J Biochem. 174:13-20. doi: 10.1093/jb/mvad025.
- Nishio K, Kawarasaki T, Sugiura Y, Matsumoto S, Konoshima A, Takano Y, Hayashi M, Okumura F, Kamura T, Mizushima T, Nakatsukasa K. (2023) Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Sci Adv. 9:eadf1956. doi: 10.1126/sciadv.adf1956.
- Matsumoto S, Endo T(2023) Proofreading of protein localization mediated by a mitochondrial AAA-ATPase Msp1. J Biochem. 173:265-271. doi: 10.1093/jb/mvac097.
2022年
- Kawamoto D, Takashima T, Fukamizo T, Numata T, Ohnuma T. (2022) A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region. Glycobiology. 32:356-364. doi: 10.1093/glycob/cwab117.
- 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: e202104076
- 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.
- Jun Tanaka, Tomoya Takashima, Naojiro Abe, Tamo Fukamizo, Tomoyuki Numata, Takayuki Ohnuma (2023) Characterization of two rice GH18 chitinases belonging to family 8 of plant pathogenesis-related proteins. Plant Sci. 326:111524 doi: 10.1016/j.plantsci.2022.111524
- Kitaoku Y, Taira T, Numata T, Ohnuma T, Fukamizo T. (2022) Structure, mechanism, and phylogeny of LysM-chitinase conjugates specifically found in fern plants. Plant Sci. 321:111310. doi: 10.1016/j.plantsci.
- Elgaabari A, Imatomi N, Kido H, Seki M, Tanaka S, Matsuyoshi Y, Nakashima T, Sawano S, Mizunoya W, Suzuki T, Nakamura M, Anderson JE, Tatsumi R. (2022) A pilot study on nitration/dysfunction of NK1 segment of myogenic stem cell activator HGF. Biochem Biophys Rep. 31:101295 doi: 10.1016/j.bbrep.2022.101295.
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