Publications 2020-2014 Shigekazu Nagata Lab.｜Biochemistry & Immunology,Immunology Frontier Research Center, Osaka University

2024～2015

Publications

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Textbook:Molecular Biology of Cells
7th edition,2022　　　　

2024

Miyata, Y., Takahashi, K., Lee, Y., Sultan, C.S., Kuribayashi, R., Takahashi, M., Hata, K., Bamba, T., Izumi, Y., Liu, K., Uemura, T., Nomura, N., Iwata, S., Nagata, S., Nishizawa, T., and Segawa, K.

TMEM63B, a mechanosensitive channel, functions as a plasma membrane lipid scramblase

Nat. Struct. Mol. Biol., 2024, in press.

DOI: https://dx.doi.org/10.1038/s41594-024-01411-6

Guillet, S., Lazarov, T., Jordan, N., Boisson, B., Tello, M., Craddock, B., Zhou, T., Nishi, C., Bareja, R., Yang, H., Rieux-Laucat, F., Irene, R., Lorenzo, F., Dyall, S.D., Isenberg, D., D’Cruz, D., Lachmann, N., Elemento, O., Viale, A., Socci, N.D., Abel, L., Nagata, S., Huse, M., Miller, W.T., Casanova, J.-L., and Geissmann, F.

ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis.

eLife. 2024

DOI: https://doi.org/10.7554/eLife.96085.2

Calianesea, D.C., Noji, T., Sullivan, J.A., Schoch, K., Shashi, V., McNiven, V., Ramos, L.L.P., Jordanova, A., Karteszi, J., Ishikita, H., and Nagata, S.

Substrate specificity controlled by the exit site of human P4-ATPases, revealed by de novo point mutations in neurological disorders.

Proc. Natl. Acad. Sci. USA, 2024, in press.

DOI: https://dx.doi.org/10.1073/pnas.2415755121

Sakuragi, T., Kanai, R., Otani, M., Kikkawa, M., Toyoshima, C., and Nagata, S.

The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase

J. Biol. Chem., 300,105755

DOI: https://dx.doi.org/10.1016/j.jbc.2024.105755

2023

Shigekazu NAGATA

Cloning of human Type I interferon cDNAs

Proc. Jpn. Acad. Ser. B., 100,1-8 (Review series to celebrate our 100th volume)

DOI: https://dx.doi.org/10.2183/pjab.100.001

Sakuragi, T. and Nagata, S.

Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases.

Nat. Rev. Mol. Cell. Biol.,Vol 24, 2023

Nature Download site

DOI: https://doi.org/10.1038/s41580-023-00604-z

2022

Miyata Y, Yamada K, Nagata S, Segawa K.

Two types of type IV P-type ATPases independently re-establish the asymmetrical distribution of phosphatidylserine in plasma membranes.

J Biol Chem: 102527, 2022

DOI: https://doi.org/10.1016/j.jbc.2022.102527

Ryoden Y, and Nagata S.

The XK plasma membrane scramblase and the VPS13A cytosolic lipid transporter for ATP-induced cell death

BioEssays August 2022

DOI: https://doi.org/10.1002/bies.202200106

Ochiai, Y., Suzuki, C., Segawa, K., Uchiyama, Y., and Nagata, S.

Inefficient development of syncytiotrophoblasts in the Atp11a-deficient mouse placenta.

Proc. Natl. Acad. Sci. U.S.A. 119: e2200582119

https://pnas.org/doi/10.1073/pnas.2200582119

Ryoden Y, Segawa K, Nagata S.

Requirement of Xk and Vps13a for the P2X7-mediated phospholipid scrambling and cell lysis in mouse T cells.

Proc Nat Acad Sci USA 119: e2119286119

https://doi.org/10.1073/pnas.2119286119

2021

Sakuragi, T., Kanai, R., Tsutsumi, A., Narita, H., Onishi, E., Nishino, K., Miyazaki, T., Baba, T., Kosako, H., Nakagawa, A., Kikkawa, M., Toyoshima, C., and Nagata, S.

The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.

Nature Structural & Molecular Biology 28: 825-834, 2021,

http://doi.org/10.1038/s41594-021-00665-8

Segawa, K., Kikuchi, A., Noji, T., Sugiura, Y., Hiraga, K., Suzuki, C., Haginoya, K., Kobayashi, Y., Matsunaga, M., Ochiai, Y., Yamada, K., Nishimura, T., Iwasawa, S., Shoji, W., Sugihara, F., Nishino, K., Kosako, H., Ikawa, M., Uchiyama, Y., Suematsu, M., Ishikita, H., Kure, S., and Nagata, S.

A sublethal ATP11A mutation associated with neurological deterioration causes aberrant phosphatidylcholine flipping in plasma membranes.

Journal of Clinical Investigation 131, e148005, 2021

http://doi.org/10.1172/jci148005

Caronni, N., Piperno, G., Simoncello, F., Romano, O., Vodret, S., Yanagihashi, Y., Dress, R., Dutertre, C.-A., Bugatti, M., Bourdely, P., Prete, A. D., Schioppa, T., Mazza, E., Collavin, L., Zacchigna, S., Ostuni, R., Guermonprez, P., Vermi, W., Ginhoux, F., Bicciato, S., Nagata, S., and Benvenu, F.

TIM4 on type 1 DCs mediates uptake of tumor-associated antigens and activation of anti tumor responses in lung tumor.

Nat Commun 12: 2237, 2021, DOI: 10.1038/s41467-021-22535-z

https://www.nature.com/articles/s41467-021-22535-z

Omori, S., Tsugita, M., Hoshikawa, Y., Morita, M., Ito, F., Yamaguchi, S.-I., Xie, Q., Noyori, O., Yamaguchi, T., Takada, A., Saitoh, T., Toyokuni, S., Akiba, H., Nagata, S., Kinoshita, K., and Nakayama, M.

Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation.

Cell Rep. 34: 108734, 2021

https://10.1016/j.celrep.2021.108734.

2020

Nakanishi, H., Nishizawa, T., Segawa, K., Nureki, O., Fujiyoshi, Y., Nagata, S., and Abe, K.

Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM.

Cell Rep. 32: 108208, 2020

https://10.1016/j.celrep.2020.108208.

Nagata, S. and Segawa, K.

Sensing and clearance of apoptotic cells

Curr. Opin. Immunol. 68: 1-8, 2020

https://doi.org/10.1016/j.coi.2020.07.007.

Nakanishi, H., Irie, K., Segawa, K., Hasegawa, K., Fujiyoshi, Y., Nagata, S., and Abe, K.

Crystal structure of a human plasma membrane phospholipid flippase.

J Biol Chem 295, 10180-10194 (2020).

https://www.jbc.org/content/295/30/10180

Ryoden, Y., Fujii, T., Segawa, K., and Nagata, S.

Functional expression of the P2X7 ATP receptor requires Eros.

J. Immunol. Vol. 204, Issue 3 559-568, 2020

https://www.jimmunol.org/content/204/3/559.long

Yamashita, Y., Suzuki, C., Uchiyama, Y., and Nagata, S.

Infertility caused by inefficient apoptotic germ cell clearance in Xkr8-deficient male mice.

Mol. Cell. Biol. 40 (3), e00402-19

https://mcb.asm.org/content/40/3/e00402-19.long

2019

Nagata, S., Sakuragi, T., and Segawa, K.

Flippase and Scramblase for Phosphatidylserine Exposure.

Curr Opin Immunol 62, 31-38 (2020).

https://doi.org/10.1016/j.coi.2019.11.009

Tsuji T, Cheng J., Tatematsu T., Ebata A., Kamikawa H., Fujita A., Gyobu S., Segawa K., Arai H., Taguchi T., Nagata S., and Fujimoto T.

Predominant localization of phosphatidylserine at the cytoplasmic leaflet of the ER, and its TMEM16K-dependent redistribution.

Proc Natl Acad Sci USA 116:13368-13373, 2019

https://www.pnas.org/content/116/27/13368

Nishi, C., Yanagihashi, Y., Segawa, K., and Nagata, S.

MERTK tyrosine kinase receptor together with TIM4 phosphatidylserine receptor mediates distinct signal transduction pathways for efferocytosis and cell proliferation.

J Biol Chem. 294(18): 7221-7230. 2019

http://www.jbc.org/cgi/doi/10.1074/jbc.RA118.006628

Sakuragi, T., Kosako, H., and Nagata, S.

Phosphorylation-mediated activation of mouse Xkr8 scramblase for phosphatidylserine exposure.

Proc. Natl. Acad. Sci. USA 116: 2907-2912, 2019

https://doi.org/10.1073/pnas.1820499116

2018

Segawa, K., Yanagihashi, Y., Yamada, K., Suzuki, C., Uchiyama, Y., and Nagata, S.

Phospholipid flippases enable precursor B cells to flee engulfment by macrophages.

Proc. Nat. Acad. Sci. USA: 115(48):12212-12217. 2018

https://doi.org/10.1073/pnas.1814323115

Kawano, M., and Nagata, S.

Efferocytosis and autoimmune disease.

Int. Immunol. 30: 551-558, 2018

https://doi.org/10.1093/intimm/dxy055

Watanabe, R., Sakuragi, T., Noji, H., and Nagata, S.

Single-molecule analysis of phospholipid scrambling by TMEM16F.

Proc. Nat. Acad. Sci. USA: 15: 3066-3071. 2018

http://doi.org./10.1073/pnas.1717956115

Galluzzi, L., Vitale, I., Aaronson, S. A., Abrams, J. M., Adam, D., Agostinis, P., Alnemri, E. S., Altucci, L., Amelio, I., Andrews, D. W., Annicchiarico-Petruzzelli, M., Antonov, A. V., Arama, E., Baehrecke, E. H., Barlev, N. A., Bazan, N. G., Bernassola, F., Bertrand, M. J. M., Bianchi, K., Blagosklonny, M. V., Blomgren, K., Borner, C., Boya, P., Brenner, C., Campanella, M., Candi, E., Carmona-Gutierrez, D., Cecconi, F., Chan, F. K., Chandel, N. S., Cheng, E. H., Chipuk, J. E., Cidlowski, J. A., Ciechanover, A., Cohen, G. M., Conrad, M., Cubillos-Ruiz, J. R., Czabotar, P. E., D'Angiolella, V., Dawson, T. M., Dawson, V. L., De Laurenzi, V., De Maria, R., Debatin, K. M., DeBerardinis, R. J., Deshmukh, M., Di Daniele, N., Di Virgilio, F., Dixit, V. M., Dixon, S. J., Duckett, C. S., Dynlacht, B. D., El-Deiry, W. S., Elrod, J. W., Fimia, G. M., Fulda, S., Garcia-Saez, A. J., Garg, A. D., Garrido, C., Gavathiotis, E., Golstein, P., Gottlieb, E., Green, D. R., Greene, L. A., Gronemeyer, H., Gross, A., Hajnoczky, G., Hardwick, J. M., Harris, I. S., Hengartner, M. O., Hetz, C., Ichijo, H., Jaattela, M., Joseph, B., Jost, P. J., Juin, P. P., Kaiser, W. J., Karin, M., Kaufmann, T., Kepp, O., Kimchi, A., Kitsis, R. N., Klionsky, D. J., Knight, R. A., Kumar, S., Lee, S. W., Lemasters, J. J., Levine, B., Linkermann, A., Lipton, S. A., Lockshin, R. A., Lopez-Otin, C., Lowe, S. W., Luedde, T., Lugli, E., MacFarlane, M., Madeo, F., Malewicz, M., Malorni, W., Manic, G., Marine, J. C., Martin, S. J., Martinou, J. C., Medema, J. P., Mehlen, P., Meier, P., Melino, S., Miao, E. A., Molkentin, J. D., Moll, U. M., Munoz-Pinedo, C., Nagata, S., Nunez, G., Oberst, A., Oren, M., Overholtzer, M., Pagano, M., Panaretakis, T., Pasparakis, M., Penninger, J. M., Pereira, D. M., Pervaiz, S., Peter, M. E., Piacentini, M., Pinton, P., Prehn, J. H. M., Puthalakath, H., Rabinovich, G. A., Rehm, M., Rizzuto, R., Rodrigues, C. M. P., Rubinsztein, D. C., Rudel, T., Ryan, K. M., Sayan, E., Scorrano, L., Shao, F., Shi, Y., Silke, J., Simon, H. U., Sistigu, A., Stockwell, B. R., Strasser, A., Szabadkai, G., Tait, S. W. G., Tang, D., Tavernarakis, N., Thorburn, A., Tsujimoto, Y., Turk, B., Vanden Berghe, T., Vandenabeele, P., Vander Heiden, M. G., Villunger, A., Virgin, H. W., Vousden, K. H., Vucic, D., Wagner, E. F., Walczak, H., Wallach, D., Wang, Y., Wells, J. A., Wood, W., Yuan, J., Zakeri, Z., Zhivotovsky, B., Zitvogel, L., Melino, G., and Kroemer, G.

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Cell Death Differ 25: 486-541. 2018

Kawano, K. and Nagata, S.

Lupus-like autoimmune disease caused by a lack of Xkr8, a caspase-dependent phospholipid scramblase

Proc. Natl. Acad. Sci. USA, 115: 2132-2137. 2018

https://doi.org/10.1073/pnas.1720732115.

Nagata S.

Apoptosis and clearance of apoptotic cells

Annual Review of Immunology 36: 489-517, 2018

https://doi.org/10.1146/annurev-immunol-042617-053010

Segawa K, Kurata S, Nagata S.

The CDC50A extracellular domain is required for forming a functional complex with and chaperoning phospholipid flippases to the plasma membrane.

J Biol Chem. 293: 2172-2182. 2018

https://doi.org/10.1074/jbc.RA117.000289.

2017

Yanagihashi Y, Segawa K, Maeda R, Nabeshima Y-i, and Nagata S.

Mouse macrophages show different requirements for phosphatidylserine receptor Tim4 in efferocytosis.

Proc Nat Acad Sci USA 114: 8800-8805.

https://doi.org/10.1073/pnas.1705365114.

Gyobu S, Ishihara K, Suzuki J, Segawa K, and Nagata S.

Characterization of the scrambling domain of the TMEM16 family.

Proc. Natl. Acad. Sci. USA 114:6274-6279.

http://www.ncbi.nlm.nih.gov/pubmed/28559311

Nagata, S. and Tanaka, M.

Programmed cell death and the immune system.

Nat Rev Immunol 17:333-340

http://www.ncbi.nlm.nih.gov/pubmed/28163302

Nakaya, M., Watari, K., Tajima, M., Nakaya, T., Matsuda, S., Ohara, H., Nishihara, H., Yamaguchi, H., Hashimoto, A., Nishida, M., Nagasaka, A., Horii, Y., Ono, H., Iribe, G., Inoue, R., Tsuda, M., Inoue, K., Tanaka, A., Kuroda, M., Nagata, S., and Kurose, H.

Cardiac myofibroblast engulfment of dead cells facilitates recovery after myocardial infarction.

J Clin Invest: 127: 383-401, 2017

http://www.ncbi.nlm.nih.gov/pubmed/27918308

2016

Cardiac myofibroblast engulfment of dead cells facilitates recovery after myocardial infarction.

J Clin Invest: in press, 2016

http://www.ncbi.nlm.nih.gov/pubmed/27918308

Suzuki, J., Imanishi, E., and Nagata, S.

Xkr8 phospholipid scrambling complex in apoptotic phosphatidylserine exposure.

Proc. Natl. Acad. Sci. USA 113: 9509-9514, 2016

http://www.ncbi.nlm.nih.gov/pubmed/27503893

Sakamoto, K., Fukushima, Y., Ito, K., Matsuda, M., Nagata, S., Minato, N., and Hattori, M.

Osteopontin in Spontaneous Germinal Centers Inhibits Apoptotic Cell Engulfment and Promotes Anti-Nuclear Antibody Production in Lupus-Prone Mice.

J. Immunol. 197: 2177-2186, 2016

http://www.ncbi.nlm.nih.gov/pubmed/7534552

Ishihara, K., Suzuki, J. and Nagata, S.

A Role of Ca2+ in the Stability and Function of TMEM16F and 16K.

Biochemistry 55: 3180-3188, 2016

http://www.ncbi.nlm.nih.gov/pubmed/27227820

Nagata, S.

Cell biology: Killer enzymes tethered.

Nature 533: 474-476, 2016

http://www.nature.com/nature/journal/v533/n7604/full/nature18439.html

Segawa, K., Kurata, S., and Nagata, S.

Human type IV P-type ATPases that work as plasma membrane phospholipid flippases, and their regulation by caspase and calcium.

J. Biol. Chem. 291 (2): 762-772, 2016

http://www.jbc.org/cgi/doi/10.1074/jbc.M115.690727

Gyobu, S., Miyata, H., Ikawa, M., Yamazaki, D., Takeshima, H., Suzuki, J., and Nagata, S.

A role of TMEM16E carrying a scrambling domain in sperm motility.

Mol. Cell Biol. 36: 645-659, 2016

http://www.ncbi.nlm.nih.gov/pubmed/26667038

Nagata, S., Suzuki, J., Segawa, K., and Fujii, T.

Exposure of Phosphatidylserine on the Cell Surface.

Cell Death Differ. 23: 952-961, 2016

http://www.ncbi.nlm.nih.gov/pubmed/26891692

2015

Fujii, T., Sakata, A., Nishimura, S., Eto, K., and Nagata, S.

TMEM16F is required for phosphatidylserine exposure and microparticle release in activated mouse platelets.

Proc. Natl. Acad. Sci. USA 112 (41): 12800-12805, 2015

http://www.pnas.org/lookup/doi/10.1073/pnas.1516594112

Segawa, K., and Nagata, S.

An apoptotic 'eat me' signal: phosphatidylserine exposure.

Trends Cell Biol 25: 649-650, 2015

http://www.ncbi.nlm.nih.gov/pubmed/26437594

Toda, S., Nishi, C., Yanagihashi, Y., Segawa, K., and Nagata, S.

Clearance of Apoptotic Cells and Pyrenocytes.

Curr. Top. Dev. Biol. 114: 267-295, 2015

http://www.ncbi.nlm.nih.gov/pubmed/26431571

Motani, K., Ito, S., and Nagata, S.

DNA-Mediated Cyclic GMP-AMP Synthase-Dependent and -Independent Regulation of Innate Immune Responses.

J Immunol. 194(10):4914-23., 2015

http://www.ncbi.nlm.nih.gov/pubmed/25855353

2002～2000

2006～2003

2014～2007

2024～2015