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Otomo, Takanori
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Otomo, Takanori

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Positions

  • 2018 - Associate Professor, Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2007 - Faculty Member, Skaggs Graduate School of Chemical and Biological Sciences , Scripps Research
  • 2013 - 2018 Assistant Professor, Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2007 - 2012 Assistant Professor, Molecular Biology , Scripps Research
Dr. Takanori Otomo studies structure and function of proteins involved in the autophagic pathway.

Contact

  • totomo@scripps.edu

Websites

  • Takanori Otomo, Ph.D.
  • Otomo Laboratory
  • Publications
  • Research
  • Background
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Publications

recent publications
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  • academic article

    • Flood, D. T., Hintzen, J. C. J., Knouse, K. W., Hill, D. E., Lu, C. X., Cistrone, P. A., Chen, J. S., Otomo, T., Dawson, P. Selenomethionine as an expressible handle for bioconjugations Proceedings of the National Academy of Sciences of the United States of America  2021 118  DOI:10.1073/pnas.2005164118  PMID:33602807  PMCID:PMC7923357
    • Fan, S. J., Yue, L. Y., Wan, W., Zhang, Y. Y., Zhang, B. D., Otomo, C., Li, Q. F., Lin, T. T., Hu, J. C., Xu, P., Zhu, M. R., Tao, H. R., et al. Inhibition of Autophagy by a Small Molecule through Covalent Modification of the LC3 Protein Angewandte Chemie-International Edition  2021  DOI:10.1002/anie.202109464  PMID:34590387  PMCID:PMC8845813
    • Maeda, S., Yamamoto, H., Kinch, L. N., Garza, C., Takahashi, S., Otomo, C., Grishin, N. V., Forli, S., Mizushima, N., Otomo, T. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A Nature Structural & Molecular Biology  2020 27:1194-1201  DOI:10.1038/s41594-020-00520-2  PMID:33106659  PMCID:PMC7718406
    • Otomo, T., Maeda, S. ATG2A transfers lipids between membranes in vitro Autophagy  2019 11:2031-2032  DOI:10.1080/15548627.2019.1659622  PMID:31441376
    • Maeda, S., Otomo, C., Otomo, T. The autophagic membrane tether ATG2A transfers lipids between membranes Elife  2019 8  DOI:10.7554/eLife.45777  PMID:31271352  PMCID:PMC6625793
    • Chowdhury, S., Otomo, C., Leitner, A., Ohashi, K., Aebersold, R., Lander, G. C., Otomo, T. Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex Proceedings of the National Academy of Sciences of the United States of America  2018 115:E9792-E9801  DOI:10.1073/pnas.1811874115  PMID:30185561  PMCID:PMC6196511
    • Ohashi, K., Otomo, T. Identification and characterization of the linear region of ATG3 that interacts with ATG7 in higher eukaryotes Biochemical and Biophysical Research Communications  2015 463:447-452  DOI:10.1016/j.bbrc.2015.05.107  PMID:26043688  PMCID:PMC4507496
    • Metlagel, Z., Otomo, C., Ohashi, K., Takaesu, G., Otomo, T. Structural insights into E2-E3 interaction for LC3 lipidation Autophagy  2014 10:522-523  DOI:10.4161/auto.27594  PMID:24413923  PMCID:PMC4077891
    • Metlagel, Z., Otomo, C., Takaesu, G., Otomo, T. Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12 Proceedings of the National Academy of Sciences of the United States of America  2013 110:18844-18849  DOI:10.1073/pnas.1314755110  PMID:24191030  PMCID:PMC3839761
    • Otomo, C., Metlagel, Z., Takaesu, G., Otomo, T. Structure of the human ATG12 similar to ATG5 conjugate required for LC3 lipidation in autophagy Nature Structural & Molecular Biology  2013 20:59-66  DOI:10.1038/nsmb.2431  PMID:23202584  PMCID:PMC3540207
    • Otomo, T., Tomchick, D. R., Otomo, C., Machius, M., Rosen, M. K. Crystal structure of the Formin mDia1 in autoinhibited conformation PLoS One  2010 5:e12896  DOI:10.1371/journal.pone.0012896  PMID:20927343  PMCID:PMC2948019
    • Shemesh, T., Otomo, T., Rosen, M. K., Bershadsky, A. D., Kozlov, M. M. A novel mechanism of actin filament processive capping by formin: Solution of the rotation paradox Journal of Cell Biology  2005 170:889-893  DOI:10.1083/jcb.200504156  PMID:16157699  PMCID:PMC2171452
    • Otomo, T., Otomo, C., Tomchick, D. R., Machius, M., Rosen, M. K. Structural basis of Rho GTPase-mediated activation of the formin rndia1 Molecular Cell  2005 18:273-281  DOI:10.1016/j.molcel.2005.04.002  PMID:15866170
    • Otomo, T., Tomchick, D. R., Otomo, C., Panchal, S. C., Machius, M., Rosen, M. K. Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain Nature  2005 433:488-494  DOI:10.1038/nature03251  PMID:15635372
    • Seth, A., Otomo, T., Yin, H. L., Rosen, M. K. Rational design of genetically encoded fluorescence resonance energy transfer-based sensors of cellular Cdc42 signaling Biochemistry  2003 42:3997-4008  DOI:10.1021/bi026881z  PMID:12680752
    • Otomo, T., Yamazaki, T., Murakami, K., Ishihama, A., Kyogoku, Y. Structural study of the N-terminal domain of the alpha subunit of escherichia coli RNA polymerase solubilized with non-denaturing detergents Journal of Biochemistry  2000 128:337-344  PMID:10920271
    • Otomo, T., Sakahira, H., Uegaki, K., Nagata, S., Yamazaki, T. Structure of the heterodimeric complex between CAD domains of CAD and ICAD Nature Structural Biology  2000 7:658-662  DOI:10.1038/77957  PMID:10932250
    • Uegaki, K., Otomo, T., Sakahira, H., Shimizu, M., Yumoto, N., Kyogoku, Y., Nagata, S., Yamazaki, T. Structure of the CAD domain of caspase-activated DNase and interaction with the CAD domain of its inhibitor Journal of Molecular Biology  2000 297:1121-1128  DOI:10.1006/jmbi.2000.3643  PMID:10764577
    • Won, H. S., Yamazaki, T., Lee, T. W., Jee, J. G., Yoon, M. K., Park, S. H., Otomo, T., Aiba, H., Kyogoku, Y., Lee, B. J. Backbone NMR assignments of a high molecular weight protein (47 kDa), cyclic AMP receptor protein (apo-CRP) Journal of Biomolecular NMR  2000 16:79-80  DOI:10.1023/a:1008398103476  PMID:10718614
    • Otomo, T., Ito, N., Kyogoku, Y., Yamazaki, T. NMR observation of selected segments in a larger protein: Central-segment isotope labeling through intein-mediated ligation Biochemistry  1999 38:16040-16044  DOI:10.1021/bi991902j  PMID:10587426
    • Otomo, T., Teruya, K., Uegaki, K., Yamazaki, T., Kyogoku, Y. Improved segmental isotope labeling of proteins and application to a larger protein Journal of Biomolecular NMR  1999 14:105-114  DOI:10.1023/a:1008308128050  PMID:10427740
    • Yamazaki, T., Otomo, T., Oda, N., Kyogoku, Y., Uegaki, K., Ito, N., Ishino, Y., Nakamura, H. Segmental isotope labeling for protein NMR using peptide splicing Journal of the American Chemical Society  1998 120:5591-5592  DOI:10.1021/ja980776o
    • Jeon, Y. H., Yamazaki, T., Otomo, T., Ishihama, A., Kyogoku, Y. Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain Journal of Molecular Biology  1997 267:953-962  DOI:10.1006/jmbi.1997.0902  PMID:9135123
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Research

research overview

  • Structural Cell Biology of the Autophagic Pathway

    Research in the Otomo laboratory is focused on elucidation of the structural and functional bases of proteins involved in autophagy. Autophagy is the intracellular degradation-recycling mechanism in eukaryotes, which utilizes membrane-bound vesicles called autophagosomes for delivery of cytoplasmic fractions including aberrant proteins and organelles to lysosomes. In recent years, studies have shown that autophagy plays major roles in human health and diseases, such as aging, cancer, neurodegenerative disorders, and infections.

    Our goal is to provide the mechanistic bases of the autophagic proteins and explain how autophagosomes are generated. We employ structural and biophysical methods, such as X-ray crystallography and NMR spectroscopy, to study physical bases of proteins, and supplement the resulting understandings with functional studies using biochemistry and cell biology.

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Background

education and training

  • Ph.D., Osaka University 2001
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Contact

full name

  • Takanori Otomo

geographic location

  • Scripps California 

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