[Publication (*Corresponding author)]
*Nishimura T, *Tsuboyama K, Nakagaki Y, Yamamoto E, Mizushima N. Rational engineering of lipid-binding probes via high-throughput protein-lipid interaction screening. bioRxiv (2025) https://www.biorxiv.org/content/10.1101/2025.01.05.627504v1
Gubas A, Attridge E, Jefferies HB, Nishimura T, Razi M, Kunzelmann S, Gilad Y, Mercer TJ, Wilson MM, Kimchi A, Tooze SA. WIPI2b recruitment to phagophores and ATG16L1 binding are regulated by ULK1 phosphorylation. EMBO Rep. 25, 3789-3811 (2024).
Nishimura T, Lazzeri G, Tooze SA, *Covino R. ATG3 proteins possess a unique amphipathic α-helix essential for the Atg8/LC3 lipidation reaction. Autophagy, 20, 212-213 (2024).
Zhang W, Nishimura T, Tooze SA. Real-Time Monitoring of ATG8 Lipidation in vitro Using Fluorescence Spectroscopy. Bio Protoc. 14, e4917 (2024).
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 b-propeller associated neurodegeneration. Hum. Mol. Genet., ddad096. (2023).
*#Nishimura T, #Lazzeri G, Mizushima N, *Covino R, Tooze SA. Unique Amphipathic alpha-helix Drives Membrane Insertion and Enzymatic Activity of ATG3. Sci. Adv., 9(25), eadh1281. (2023).
#Zhang W, #Nishimura T, Gahlot D, Saito C, Davis C, Jefferies HBJ, Schreiber A, Thukral L, *Tooze SA. Autophagosome membrane expansion is mediated by the N-terminus and cis-membrane association of human ATG8s. eLife, e89185. (2023).
*Tooze SA, Zhang W, Lazzeri G, Gahlot D, Thukral L, Covino R, Nishimura T. Membrane association of the ATG8 conjugation machinery emerges as a key regulatory feature for autophagosome biogenesis. FEBS Lett. (2023). doi: 10.1002/1873-3468.14676.
#Chen Z, #Malia PC, #Hatakeyama R, Nicastro R, Hu Z, Peli-Gulli MP, Gao J, Nishimura T, Eskes E, Stefan CJ, Winderickx J, *De Virgilio C, *Ungermann C. TORC1 Determines Fab1 Lipid Kinase Function at Signaling Endosomes and Vacuoles. Curr. Biol., 31, 297-309.e8. (2021).
*Nishimura T. A real-time phosphatidylinositol 4-phosphate 5-kinase assay using fluorescence spectroscopy. Methods Molecular Biology, 2251, 121-132 (2021).
*Nishimura T, *Tooze SA. Emerging roles of ATG proteins and membrane lipids in autophagosome formation. Cell Discovery, 6, 32 (2020).
*Nishimura T, *Stefan CJ. Specialized ER Membranes Domains for Lipid Metabolism and Transport. BBA-Molecular and Cell Biology of Lipids, 1865, pii:1388-1981(19)30121-0 (2020).
Morishita H, Zhao YG, Tamura N, Nishimura T, Kanda Y, Sakamaki Y, Okazaki M, Li D, *Mizushima N. A critical role of VMP1 in lipoprotein secretion. eLife, 8, e48834 (2019).
*Nishimura T, Gecht M, Covino R, Hummer G, Surma MA, Klose C, Arai H, Kono N, *Stefan CJ. Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 Synthesis. Molecular Cell, 75, 1043-1057 (2019).
Malia PC, Numrich J, Nishimura T, Montoro AG, Stefan C, *Ungermann C. Control of vacuole membrane homeostasis by a resident PI-3,5-kinase inhibitor. Proc Natl Acad Sci USA., 115, 4684-4689 (2018).
*Nishimura T, *Mizushima N. The ULK complex initiates autophagosome formation at phosphatidylinositol synthase-enriched ER subdomains. Autophagy, 13, 1795-1796 (2017).
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., 591, 3819-3830 (2017).
*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., 36, 1719-1735 (2017).
Uematsu M, Nishimura T, Sakamaki Y, Yamamoto H, *Mizushima N. Accumulation of undegraded autophagosomes by expression of dominant-negative STX17 (syntaxin 17) mutants. Autophagy, 13, 1452-1464 (2017).
Morita M, Sekine A, Urano Y, Nishimura T, Takabe W, Arai H, Hamakubo T, Kodama T, *Noguchi N. Lysophosphatidylcholine promotes SREBP-2 activation via rapid cholesterol efflux and SREBP-2-independent cytokine release in human endothelial cells. J. Biochem., 158, 331-338 (2015).
Jiang P, Nishimura T, Sakamaki Y, Itakura E, Hatta T, Natsume T, *Mizushima N. The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. Mol. Biol. Cell. 25, 1327-1337 (2014).
Udagawa O, Ito C, Ogonuki N, Sato H, Lee S, Pearlta T, Ichi I, Uchida Y, Nishimura T, Murakami M, Ogura A, Inoue T, *Toshimori K, *Arai H. Oligo-astheno-teratozoosermia in mice lacking ORP4, a sterol-binding protein in the OSBP-related protein family. Genes Cells. 19, 13-27 (2014).
Nishimura T, Uchida Y, Yachi R, Kudlyk T, Lupashin V, Inoue T, Taguchi T, *Arai H. Oxysterol-binding protein (OSBP) is required for the perinuclear localization of intra-Golgi v-SNAREs. Mol. Biol. Cell. 24, 3534-3544 (2013).
*#Saitsu H, #Nishimura T, #Muramatsu K, Kodera H, Kumada S, Sugai K, Kasai-Yoshida E, Sawaura N, Nishida H, Hoshino A, Ryujin F, Yoshioka S, Nishiyama K, Kondo Y, Tsurusaki Y, Nakashima M, Miyake N, Arakawa H, Kato M, *Mizushima N, *Matsumoto N. De novo mutations in the autophagy gene WDR45 cause static encephalopathy of childhood with neurodegeneration in adulthood. Nature Genet. 45, 445-449 (2013).
Nishimura T, Kaizuka T, Cadwell K, Sahani MH, Saitoh T, Akira S, Virgin HW, *Mizushima N. FIP200 regulates targeting of Atg16L1 to the isolation membrane. EMBO Rep. 14, 284-291 (2013).
*#Yasui T, #Sakakibara-Yada K, Nishimura T, Morita K, Tada S, Mosialos G, *Kieff E, *Kikutani H. Protein kinase N1, a cell inhibitor of Akt kinase, has a central role in quality control of germinal center formation. Proc Natl Acad Sci USA. 109, 21022-21027 (2012).
#Velikkakath AK, #Nishimura T, Oita E, Ishihara N, *Mizushima N. Mammalian Atg2 proteins are essential for autophagosome formation and important for regulation of size and distribution of lipid droplets. Mol. Biol. Cell. 23, 896-909 (2012).
Shibata M, Yoshimura K, Tamura H, Ueno T, Nishimura T, Inoue T, Sasaki M, Koike M, Arai H, Kominami E, *Uchiyama Y. LC3, a microtubule-associated protein1A/B light chain3, is involved in cytoplasmic lipid droplet formation. Biochem. Biophys. Res. Commun. 393, 274-279 (2010).
Maekawa M, Inoue T, Kobuna H, Nishimura T, Gengyo-Ando K, Mitani S, *Arai H. Functional analysis of GS28, an intra-Golgi SNARE, in Caenorhabditis elegans. Genes Cells. 14, 1003-1013 (2009).
Nishimura T, Inoue T, Shibata N, Sekine A, Takabe W, Noguchi N, *Arai H. Inhibition of cholesterol biosynthesis by 25-hydroxycholesterol is independent of OSBP. Genes Cells. 10, 793-801 (2005).
[和文総説＆紹介記事]
*西村多喜：北から南から 生化学会, Vol. 96 (6), 875-876, 2024年
*西村多喜：脂質交換タンパク質が司るナノスケールの脂質膜環境 生物物理, Vol. 62 (3), 170-174, 2022年
[特許申請済み]
西村多喜, 坪山幸太郎 2024年
坪山幸太郎, 西村多喜 2024年
西村多喜 2023年