Mashita T., Kowada T., Yamamoto H., Hamaguchi S., Toshizo Sato, Matsui T., Mizukami S.*
Quantitative and repetitive control of subcellular protein-protein interaction using a photochromic dimerizer
Nat. Chem. Biol. (2024) doi: 10.1038/s41589-024-01654-w

Shinoda S., Sakai Y., Matsui T., Uematsu M., Koyama-Honda I., Sakamaki J., Yamamoto H., Mizushima N.*
Syntaxin 17 recruitment to mature autophagosomes is temporally regulated by PI4P accumulation
eLife (2024) doi: 10.7554/eLife.92189.1

Yamamoto H.*, Matsui T.
Molecular mechanisms of macroautophagy, microautophagy, and chaperone-mediated autophagy
J. Nippon Med. Sch. (2024) doi: 10.1272/jnms.JNMS.2024_91-102

Yamamoto H., Zhang S., Mizushima N.*
Autophagy genes in biology and disease
Nat. Rev. Genet. (2023) doi: 10.1038/s41576-022-00562-w

Shimizu T., Tamura N., Nishimura T., Saito C., Yamamoto H., Mizushima N.*
Comprehensive analysis of autophagic functions of WIPI family proteins and their implications for the pathogenesis of β-propeller associated neurodegeneration
Hum. Mol. Genet. (2023) doi: 10.1093/hmg/ddad096

Ohshima T., Yamamoto H., Sakamaki Y., Saito C., Mizushima N.*
NCOA4 drives ferritin phase separation to facilitate macroferritinophagy and microferritinophagy
J. Cell Biol. (2022) doi: 10.1083/jcb.202203102

Yim W.W., Yamamoto H.*, Mizushima N.*
A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag
eLife (2022) doi: 10.7554/eLife.78923

Yim W.W., Yamamoto H.*, Mizushima N.*
A HaloTag-based reporter processing assay to monitor autophagic flux
Autophagy (2022) doi: 10.1080/15548627.2022.2123638

Sakamaki J., Ode K.L., Kurikawa Y., Ueda H.R., Yamamoto H., Mizushima N.*
Ubiquitination of phosphatidylethanolamine in organellar membranes
Mol. Cell (2022) doi: 10.1016/j.molcel.2022.08.008

Fu J., Pang Y., Chen H., Yamamoto H., Lin Z., Chen Y., Li Z., Mizushima N., Jia H.*
Apicoplast biogenesis mediated by ATG8 requires the ATG12-ATG5-ATG16L and SNAP29 complexes in Toxoplasma gondii
Autophagy (2022) doi: 10.1080/15548627.2022.2123639

Zhang S., Yazaki E., Sakamoto H., Yamamoto H., Mizushima N.*
Evolutionary diversification of the autophagy-related ubiquitin-like conjugation systems
Autophagy (2022) doi: 10.1080/15548627.2022.2059168

Yim W.W., Yamamoto H., Mizushima N.*
Annexins A1 and A2 are recruited to larger lysosomal injuries independently of ESCRTs to promote repair
FEBS Lett. (2022) doi: 10.1002/1873-3468.14329

Okawa F., Hama Y., Zhang S., Morishita H., Yamamoto H., Levine T.P., Mizushima N.*
Evolution and insights into the structure and function of the DedA superfamily containing TMEM41B and VMP1
J. Cell Sci. (2021) doi: 10.1242/jcs.255877

Maeda S., Yamamoto H., Kinch L.N., Garza C.M., Takahashi S., Otomo C., Grishin N.V., Forli S., Mizushima N., Otomo T.*
Structure, lipid scrambling activity and role in autophagosome formation of ATG9A
Nat. Struct. Mol. Biol. (2020) doi: 10.1038/s41594-020-00520-2

Pang Y., Yamamoto H., Sakamoto H., Oku M., Mutungi J.K., Sahani M.H., Kurikawa Y., Kita K., Noda N.N., Sakai Y., Jia H.*, Mizushima N.*
Evolution from covalent conjugation to non-covalent interaction in the ubiquitin-like ATG12 system
Nat. Struct. Mol. Biol. (2019) doi: 10.1038/s41594-019-0204-3

Harada K., Kotani T., Kirisako H., Sakoh-Nakatogawa M., Oikawa Y., Kimura Y., Hirano H., Yamamoto H., Ohsumi Y., Nakatogawa H.*
Two distinct mechanisms target the autophagy-related E3 complex to the pre-autophagosomal structure
eLife (2019) doi: 10.7554/eLife.43088

Mizushima N.*, Matsui T., Yamamoto H.
YKT6 as a second SNARE protein of mammalian autophagosomes
Autophagy (2019) doi: 10.1080/15548627.2018.1532262

Matsui T., Jiang P., Nakano S., Sakamaki Y., Yamamoto H., Mizushima N.*
Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17
J. Cell Biol. (2018) doi: 10.1083/jcb.201712058

Tamura N., Nishimura T., Sakamaki Y., Koyama-Honda I., Yamamoto H., Mizushima N.*
Differential requirement for ATG2A domains for localization to autophagic membranes and lipid droplets
FEBS Lett. (2017) doi: 10.1002/1873-3468.12901

Uematsu M., Nishimura T., Sakamaki Y., Yamamoto H., Mizushima N.*
Accumulation of undegraded autophagosomes by expression of dominant-negative STX17 (syntaxin 17) mutants
Autophagy (2017) doi: 10.1080/15548627.2017.1327940

Nishimura T.*, Tamura N., Kono N., Shimanaka Y., Arai H., Yamamoto H., Mizushima N.*
Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains
EMBO J. (2017) doi: 10.15252/embj.201695189

Yamamoto H., Fujioka Y., Suzuki S.W., Noshiro D., Suzuki H., Kondo-Kakuta C., Kimura Y., Hirano H., Ando T., Noda N.N.*, Ohsumi Y.*
The intrinsically disordered protein Atg13 mediates supramolecular assembly of autophagy initiation complexes
Dev. Cell (2016) doi: 10.1016/j.devcel.2016.06.015

Yamamoto H.*, Shima T., Yamaguchi M., Mochizuki Y., Hoshida H., Kakuta S., Kondo-Kakuta C., Noda N.N., Itoh T., Inagaki F., Akada R., Ohsumi Y.*
The thermotolerant yeast Kluyveromyces marxianus is a useful organism for structural and biochemical studies of autophagy
J. Biol. Chem. (2015) doi: 10.1074/jbc.M115.684233

Suzuki S.W., Yamamoto H.*, Oikawa Y., Kondo-Kakuta C., Kimura Y., Hirano H., Ohsumi Y.*
Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation
Proc. Natl. Acad. Sci. (2015) doi: 10.1073/pnas.1421092112

Fujioka Y., Suzuki S.W., Yamamoto H., Kondo-Kakuta C., Kimura Y., Hirano H., Akada R., Inagaki F., Ohsumi Y.*, Noda N.N.*
Structural basis of starvation-induced assembly of the autophagy initiation complex
Nat. Struct. Mol. Biol. (2014) doi: 10.1038/nsmb.2822

Fujimoto T.*, Yamamoto H., Ohsumi Y.
Different phosphatidylinositol 3-phosphate asymmetries in yeast and mammalian autophagosomes revealed by a new electron microscopic technique
Autophagy (2014) doi: 10.4161/auto.28489

Cheng J., Fujita A., Yamamoto H., Tatematsu T., Kakuta S., Obara K., Ohsumi Y., Fujimoto T.*
Yeast and mammalian autophagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries
Nat. Commun. (2014) doi: 10.1038/ncomms4207

Suzuki K.*, Akioka M., Kondo-Kakuta C., Yamamoto H., Ohsumi Y.*
Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae
J. Cell Sci. (2013) doi: 10.1242/jcs.122960

Kakuta S., Yamamoto H., Negishi L., Kondo-Kakuta C., Hayashi N., Ohsumi Y.*
Atg9 vesicles recruit vesicle-tethering proteins Trs85 and Ypt1 to the autophagosome formation site
J. Biol. Chem. (2012) doi: 10.1074/jbc.M112.411454

Yamaguchi M., Matoba K., Sawada R., Fujioka Y., Nakatogawa H., Yamamoto H., Kobashigawa Y., Hoshida H., Akada R., Ohsumi Y., Noda N.N.*, Inagaki F.*
Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7
Nat. Struct. Mol. Biol. (2012) doi: 10.1038/nsmb.2451

Obara K., Yamamoto H., Kihara A.*
Membrane protein Rim21 plays a central role in sensing ambient pH in Saccharomyces cerevisiae
J. Biol. Chem. (2012) doi: 10.1074/jbc.M112.394205

Watanabe Y., Kobayashi T., Yamamoto H., Hoshida H., Akada R., Inagaki F., Ohsumi Y., Noda N.N.*
Structure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18
J. Biol. Chem. (2012) doi: 10.1074/jbc.M112.397570

Nakatogawa H.*, Ohbayashi S., Sakoh-Nakatogawa M., Kakuta S., Suzuki S.W., Kirisako H., Kondo-Kakuta C., Noda N.N., Yamamoto H., Ohsumi Y.
The autophagy-related protein kinase Atg1 interacts with the ubiquitin-like protein Atg8 via the Atg8 family interacting motif to facilitate autophagosome formation
J. Biol. Chem. (2012) doi: 10.1074/jbc.C112.387514

Yamamoto H., Kakuta S., Watanabe T.M., Kitamura A., Sekito T., Kondo-Kakuta C., Ichikawa R., Kinjo M., Ohsumi Y.*
Atg9 vesicles are an important membrane source during early steps of autophagosome formation
J. Cell Biol. (2012) doi: 10.1083/jcb.201202061

Yamaguchi M., Noda N.N.*, Yamamoto H., Shima T., Kumeta H., Kobashigawa Y., Akada R., Ohsumi Y., Inagaki F.*
Structural insights into Atg10-mediated formation of the autophagy-essential Atg12-Atg5 conjugate
Structure (2012) doi: 10.1016/j.str.2012.04.018

Yamamoto H., Itoh N., Kawano S., Yatsukawa Y., Momose T., Makio M., Matsunaga M., Yokota M., Esaki M., Shodai T., Kohda D., Hobbs A.E., Jensen R.E., Endo T.*
Dual role of the receptor Tom20 in specificity and efficiency of protein import into mitochondria
Proc. Natl. Acad. Sci. (2011) doi: 10.1073/pnas.1014918108

Yamamoto H., Fukui K., Takahashi H., Kitamura S., Shiota T., Terao K., Uchida M., Esaki M., Nishikawa S., Yoshihisa T., Yamano K., Endo T.*
Roles of Tom70 in import of presequence-containing mitochondrial proteins
J. Biol. Chem. (2009) doi: 10.1074/jbc.M109.041756

Tamura Y., Harada Y., Shiota T., Yamano K., Watanabe K., Yokota M., Yamamoto H., Sesaki H., Endo T.*
Tim23-Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import
J. Cell Biol. (2009) doi: 10.1083/jcb.200808068

Tamura Y., Harada Y., Yamano K., Watanabe K., Ishikawa D., Ohshima C., Nishikawa S., Yamamoto H., Endo T.*
Identification of Tam41 maintaining integrity of the TIM23 protein translocator complex in mitochondria
J. Cell Biol. (2006) doi: 10.1083/jcb.200603087

Yamamoto H., Momose T., Yatsukawa Y., Ohshima C., Ishikawa D., Sato T., Tamura Y., Ohwa Y., Endo T.*
Identification of a novel member of yeast mitochondrial Hsp70-associated motor and chaperone proteins that facilitates protein translocation across the inner membrane
FEBS Lett. (2005) doi: 10.1016/j.febslet.2004.12.018

Naoe M., Ohwa Y., Ishikawa D., Ohshima C., Nishikawa S., Yamamoto H., Endo T.*
Identification of Tim40 that mediates protein sorting to the mitochondrial intermembrane space
J. Biol. Chem. (2004) doi: 10.1074/jbc.M410272200

Esaki M., Shimizu H., Ono T., Yamamoto H., Kanamori T., Nishikawa S., Endo T.*
Mitochondrial protein import. Requirement of presequence elements and TOM components for precursor binding to the TOM complex
J. Biol. Chem. (2004) doi: 10.1074/jbc.M404591200

Ishikawa D., Yamamoto H., Tamura Y., Moritoh K., Endo T.*
Two novel proteins in the mitochondrial outer membrane mediate β-barrel protein assembly
J. Cell Biol. (2004) doi: 10.1083/jcb.200405138

Endo T.*, Yamamoto H., Esaki M.
Functional cooperation and separation of translocators in protein import into mitochondria, the double-membrane bounded organelles
J. Cell Sci. (2003) doi: 10.1242/jcs.00667

Yamamoto H., Esaki M., Kanamori T., Tamura Y., Nishikawa S., Endo T.*
Tim50 is a subunit of the TIM23 complex that links protein translocation across the outer and inner mitochondrial membranes
Cell (2002) doi: 10.1016/s0092-8674(02)01053-x