Journal Paper

• Doshun Ito, Hinata Kawamura, Akira Oikawa, Yuta Ihara, Toshio Shibata, Nobuhiro Nakamura, Tsunaki Asano, Shun-Ichiro Kawabata, Takashi Suzuki, Shinji Masuda. ppGpp functions as an alarmone in metazoa, Communications Biology, Nov. 2020.  Official location  
• Annik Jakob, Hiroshi Nakamura, Atsuko Kobayashi, Yuki Sugimoto, Annegret Wilde, Shinji Masuda. The (PATAN)-CheY-Like Response Regulator PixE Interacts with the Motor ATPase PilB1 to Control Negative Phototaxis in the Cyanobacterium Synechocystis sp. PCC 6803, Plant and Cell Physiology, Vol. 61, No. 2, pp. 296-307, Feb. 2020.  Official location  
• Kyohei Harada, Takatoshi Arizono, Ryoichi Sato, Mai Duy Luu Trinh, Akira Hashimoto, Masaru Kono, Masaru Tsujii, Nobuyuki Uozumi, Shinichi Takaichi, Shinji Masuda. DAY-LENGTH-DEPENDENT DELAYED-GREENING1, the Arabidopsis Homolog of the Cyanobacterial H+-Extrusion Protein, Is Essential for Chloroplast pH Regulation and Optimization of Non-Photochemical Quenching, Plant and Cell Physiology, Vol. 60, No. 12, pp. 2660-2671, Dec. 2019.  Official location  
• Takayuki Shimizu, Shinji Masuda. Persulphide-responsive transcriptional regulation and metabolism in bacteria, The Journal of Biochemistry, Aug. 2019.  Official location  
• Mai Duy Luu Trinh, Ryoichi Sato, Shinji Masuda. Genetic characterization of a flap1 null mutation in Arabidopsis npq4 and pgr5 plants suggests that the regulatory role of FLAP1 involves the control of proton homeostasis in chloroplasts, Photosynthesis Research, Vol. 139, No. 1-3, pp. 413-424, Mar. 2019.  Official location  
• Ryoichi Sato, Masaru Kono, Kyohei Harada, Hiroyuki Ohta, Shinichi Takaichi, Shinji Masuda. FLUCTUATING-LIGHT-ACCLIMATION PROTEIN1, Conserved in Oxygenic Phototrophs, Regulates H+ Homeostasis and Non-Photochemical Quenching in Chloroplasts, Plant and Cell Physiology, Oxford University Press, 58, 10, 1622-1630, Sept. 2018.
• Ryoichi Sato, Rinya Kawashima, Mai Duy Luu Trinh, Masahiro Nakano, Takeharu Nagai, Shinji Masuda. Significance of PGR5-dependent cyclic electron flow for optimizing the rate of ATP synthesis and consumption in Arabidopsis chloroplasts, Photosynthesis Research, Springer, pp. 1–7, June 2018.  Official location  
• Tomotsumi Fujisawa, SHINJI MASUDA. Light-induced chromophore and protein responses and mechanical signal transduction of BLUF proteins, Biophysical Reviews, Apr. 2018.  Official location  
• Rinya Kawashima, Ryoichi Sato, Kyohei Harada, Shinji Masuda. Relative contributions of PGR5- and NDH-dependent photosystem I cyclic electron flow in the generation of a proton gradient in Arabidopsis chloroplasts, Planta, Springer, Volume 246, 5, pp. 1045–1050, Nov. 2017.  Official location  
• Ryoichi Sato, Masaru Kono, Kyohei Harada, Hiroyuki Ohta, Shinichi Takaichi, Shinji Masuda. FLUCTUATING-LIGHT-ACCLIMATION PROTEIN1, Conserved in Oxygenic Phototrophs, Regulates H+ Homeostasis and Non-Photochemical Quenching in Chloroplasts, Plant and Cell Physiology, Vol. 58, No. 10, pp. 1622-1630, Oct. 2017.  Official location  
• Shinji Masuda. Significance of accumulation of the alarmone (p)ppGpp in chloroplasts for controlling photosynthesis and metabolite balance during nitrogen starvation in Arabidopsis., Photosyn. Res., July 2017.
• Doshun Ito, Yuta Ihara, Hidenori Nishihara, Shinji Masuda. Phylogenetic analysis of proteins involved in the stringent response in plant cells, Journal of Plant Research, Vol. 130, No. 4, pp. 625–634, July 2017.
• Shinji Masuda. Characterization of redox-active cysteine residues of persulfide-responsive transcriptional repressor SqrR, Commun. Integr. Biol., June 2017.
• Rina Honoki, Sumire Ono, Akira Oikawa, Kazuki Saito, Shinji Masuda. Significance of accumulation of the alarmone (p)ppGpp in chloroplasts for controlling photosynthesis and metabolite balance during nitrogen starvation in Arabidopsis, Photosynthesis Research, May 2017.
• Shinji Masuda. Phylogenetic analysis of proteins involved in the stringent response in plant cells, J. Plant Res., Mar. 2017.
• Shinji Masuda. The sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis, Proc. Natl. Acad. Sci. USA., No. 114, pp. 2355-2360, Feb. 2017.  Official location  
• Shinji Masuda. Genetics of the blue light-dependent signal cascade that controls phototaxis in the cyanobacterium Synechocystis sp. PCC6803., Plant Cell Physiology, No. 58, pp. 458-465, Jan. 2017.
• Shinji Masuda, Mikiko Tanaka. PICCORO：A technique for manipulating the activity of transcription factors with blue light., Methods in Cell Biology: The Zebrafish, 4th edition, Volume 3-Genetics, Genomics, and Transcriptomics., No. 135, pp. 289-95, Apr. 2016.
• Ihara, Y., Masuda, S.. Cytosolic ppGpp accumulation induces retarded plant growth and development., Plant Signal. Behav., Vol. 11, Jan. 2016.
• Ihara, Y., Masuda, S., SHINJI MASUDA. Cytosolic ppGpp accumulation induces retarded plant growth and development, Plant Signaling and Behavior, Vol. 11, No. 2, 2016.  Official location  
• Mikika Maekawa, Rina Honoki, Yuta Ihara, Ryoichi Sato, Akira Oikawa, Yuri Kanno, Hiroyuki Ohta, Mitsunori Seo, Kazuki Saito, Shinji Masuda. Impact of the plastidial stringent response in plant growth and stress responses., Nature plants, Vol. 1, pp. 15167, Nov. 2015.
• Shimizu, T., Cheng, Z., Matsuura, K., Masuda, S., Bauer C. E.. Evidence that altered cis element spacing affects PpsR mediated redox control of photosynthesis gene expression in Rubrivivax gelatinosus., PLos ONE, Vol. 10, June 2015.
• Yuta Ihara, Hiroyuki Ohta, Shinji Masuda. A highly sensitive quantification method for the accumulation of alarmone ppGpp in Arabidopsis thaliana using UPLC-ESI-qMS/MS, Journal of Plant Research, Springer Japan, 128, 3, 511-518, May 2015.
• SHINJI MASUDA. A highly sensitive quantification method for the accumulation of alarmone ppGpp in Arabidopsis thaliana using UPLC-ESI-qMS/MS., J. Plant Res., Vol. 128, No. 3, pp. 511-518, May 2015.  Official location  
• Tsukatani, Y., Masuda, S.. Elucidation of genetic backgrounds necessary for chlorophyll a biosynthesis toward artificial creation of oxygenic photosynthesis., Origins Life Evol. Biosph., Vol. 45, pp. 367-369, May 2015.
• Ren, S., Sugimoto, Y., Kobayashi, T., Masuda, S.. Cross-linking analysis reveals the putative dimer structure of the cyanobacterial BLUF photoreceptor PixD., FEBS Lett., Vol. 589, pp. 1879-1882, May 2015.
• Hikaru Saito, Takaya Oikawa, Shin Hamamoto, Yasuhiro Ishimaru, Miyu Kanamori-Sato, Yuko Sasaki-Sekimoto, Tomoya Utsumi, Jing Chen, Yuri Kanno, Shinji Masuda, Yuji Kamiya, Mitsunori Seo, Nobuyuki Uozumi, Minoru Ueda, Hiroyuki Ohta. The jasmonate-responsive GTR1 transporter is required for gibberellin-mediated stamen development in Arabidopsis, Nature Communications, Nature Publishing Group, 6, 6095, Feb. 2015.
• SHINJI MASUDA. The jasmonate-responsive GTR1 transporter is required for gibberellin-mediated stamen development in Arabidopsis., Nature Commun., Vol. 6, Feb. 2015.  Official location  
• Tsukatani, Y., Masuda, S., SHINJI MASUDA. Elucidation of Genetic Backgrounds Necessary for Chlorophyll a Biosynthesis Toward Artificial Creation of Oxygenic Photosynthesis, Origins of Life and Evolution of Biospheres, Vol. 45, No. 3, pp. 367-369, 2015.  Official location  
• Maekawa, M., Honoki, R., Ihara, Y., Sato, R., Oikawa, A., Kanno, Y., Ohta, H., Seo, M., Saito, K., Masuda, S., SHINJI MASUDA. Impact of the plastidial stringent response in plant growth and stress responses, Nature Plants, Vol. 1, 2015.  Official location  
• Shimizu, T., Cheng, Z., Matsuura, K., Masuda, S., Bauer, C.E., SHINJI MASUDA. Evidence that altered cis element spacing affects PpsR mediated redox control of photosynthesis gene expression in Rubrivivax gelatinosus, PLoS ONE, Vol. 10, No. 6, 2015.  Official location  
• Ren, S., Sugimoto, Y., Kobayashi, T., Masuda, S., SHINJI MASUDA. Cross-linking analysis reveals the putative dimer structure of the cyanobacterial BLUF photoreceptor PixD, FEBS Letters, Vol. 589, No. 15, pp. 1879-1882, 2015.  Official location  
• Fujisawa, T., Takeuchi, S., Masuda, S., Tahara, T.. Signaling-state formation mechanism of a BLUF protein PapB from the purple bacterium Rhodopseudomonas palustris studied by femtosecond time-resolved absorption spectroscopy., J. Phys. Chem. B, Vol. 118, pp. 14761-14773, Nov. 2014.
• Masanori Satoh, Yoshihito Tokaji, Atsushi J. Nagano, Ikuko Hara-Nishimura, Makoto Hayashi, Mikio Nishimura, Hiroyuki Ohta, Shinji Masuda. Arabidopsis mutants affecting oxylipin signaling in photo-oxidative stress responses, Plant Physiology and Biochemistry, Vol. 81, pp. 90-95, Aug. 2014.
• Ryoichi Sato, Hiroyuki Ohta, Shinji Masuda. Prediction of respective contribution of linear electron flow and PGR5-dependent cyclic electron flow to non-photochemical quenching induction, Plant Physiology and Biochemistry, Vol. 81, pp. 190-196, Aug. 2014.
• Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H, Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T, Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Mie Shimojima, Shinji Masuda, Masako Iwai, Takashi Nobusawa, Takafumi Narise, Satoshi Kondo, Hikaru Saito, Ryoichi Sato, Masato Murakawa, Yuta Ihara, Yui Oshima-Yamada, Kinuka Ohtaka, Masanori Satoh, Kohei Sonobe, Midori Ishii, Ryosuke Ohtani, Miyu Kanamori-Sato, Rina Honoki, Daichi Miyazaki, Hitoshi Mochizuki, Jumpei Umetsu, Kouichi Higashi, Daisuke Shibata, Yuji Kamiya, Naoki Sato, Yasukazu Nakamura, Satoshi Tabata, Shigeru Ida, Ken Kurokawa, Hiroyuki Ohta. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation., May 2014.  Official location  
• Yuzawa, Y., Shimojima, M., Sato, R., Mizusawa, N., Ikeda, K., Suzuki, M., Iwai, M., Hori, K., Wada, H., Masuda, S., Ohta, H.. Cyanobacterial monogalactosyldiacylglycerol-synthesis pathway is involved in normal unsaturation of galactolipids and low-temperature adaptation of Synechocystis sp. PCC 6803., Biochim. Biophys. Acta, Vol. 1841, pp. 475-483, Apr. 2014.  Official location  
• Shinji Masuda, Yoshihito Tokaji, Yuichi Kobayashi, Hiroyuki Ohta. Mechanisms of induction of the stress-responsive transcription factors HsfA2 and DREB2A by 12-oxo-phytodienoic acid in Arabidopsis thaliana., Bioscience, biotechnology, and biochemistry, Apr. 2014.
• Sato, R., Ohta, H., Masuda, S.. Prediction of respective contribution of linear electron flow and PGR5-dependent cyclic electron flow to non-photochemical quenching induction., Plant Physiol. Biochem., Vol. 81, pp. 190-196, Mar. 2014.
• Yuko Sasaki-Sekimoto, Hikaru Saito, Shinji Masuda, Ken Shirasu, Hiroyuki Ohta. Comprehensive analysis of protein interactions between JAZ proteins and bHLH transcription factors that negatively regulate jasmonate signaling., Plant signaling & behavior, Vol. 9, Jan. 2014.
• SHINJI MASUDA. Cyanobacterial monogalactosyldiacylglycerol-synthesis pathway is involved in normal unsaturation of galactolipids and low-temperature adaptation of Synechocystis sp. PCC 6803., Biochim. Biophys. Acta 1841: 475-483., 2014.
• SHINJI MASUDA. Arabidopsis mutants affecting oxylipin signaling in photo-oxidative stress responses., Plant Physiol. Biochem. 81: 90-95., 2014.
• Sasaki-Sekimoto, Y., Saito, H., Masuda, S., Shirasu, K., Ohta, H., SHINJI MASUDA. Comprehensive analysis of protein interactions between JAZ proteins and BHLH transcription factors that negatively regulate jasmonate signaling, Plant Signaling and Behavior, Vol. 9, No. JAN, 2014.  Official location  
• SHINJI MASUDA. Comprehensive analysis of protein interactions between JAZ proteins and bHLH transcription factors that negatively regulate jasmonate signaling., Plant Signaling Behavior 9, e27639., 2014.
• Yuzawa, Y., Shimojima, M., Sato, R., Mizusawa, N., Ikeda, K., Suzuki, M., Iwai, M., Hori, K., Wada, H., Masuda, S., Ohta, H., SHINJI MASUDA. Cyanobacterial monogalactosyldiacylglycerol-synthesis pathway is involved in normal unsaturation of galactolipids and low-temperature adaptation of Synechocystis sp. PCC 6803, Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, Vol. 1841, No. 4, pp. 475-483, 2014.  Official location  
• SHINJI MASUDA. Klebsormidium flaccidum gemone reveals primary factors for plant terrestrial adaptation., Nature Commun. 5: 3978., 2014.
• Hori, K., Maruyama, F., Fujisawa, T., Togashi, T., Yamamoto, N., Seo, M., Sato, S., Yamada, T., Mori, H., Tajima, N., Moriyama, T., Ikeuchi, M., Watanabe, M., Wada, H., Kobayashi, K., Saito, M., Masuda, T., Sasaki-Sekimoto, Y., Mashiguchi, K., Awai, K., Shimojima, M., Masuda, S., Iwai, M., Nobusawa, T., Narise, T., Kondo, S., Saito, H., Sato, R., Murakawa, M., Ihara, Y., Oshima-Yamada, Y., Ohtaka, K., Satoh, M., Sonobe, K., Ishii, M., Ohtani, R., Kanamori-Sato, M., Honoki, R., Miyazaki, D., Mochizuki, H., Umetsu, J., Higashi, K., Shibata, D., Kamiya, Y., Sato, N., Nakamura, Y., Tabata, S., Ida, S., Kurokawa, K., Ohta, H., SHINJI MASUDA. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation, Nature Communications, Vol. 5, 2014.  Official location  
• Masuda, S., Tokaji, Y., Kobayashi, Y., Ohta, H., SHINJI MASUDA. Mechanisms of induction of the stress-responsive transcription factors HsfA2 and DREB2A by 12-oxo-phytodienoic acid in Arabidopsis thaliana, Bioscience, Biotechnology and Biochemistry, Vol. 78, No. 4, pp. 647-650, 2014.  Official location  
• SHINJI MASUDA. Mechanisms of induction of the stress-responsive transcription factors HsfA2 and DREB2A by 12-oxo-phytodienoic acid in Arabidopsis thaliana., Biosci. Biotech. Biochem. 78: 647-650., 2014.
• SHINJI MASUDA. Prediction of respective contribution of linear electron flow and PGR5-dependent cyclic electron flow to non-photochemical quenching induction., Plant Physiol. Biochem. 81: 190-196., 2014.
• Fujisawa, T., Takeuchi, S., Masuda, S., Tahara, T., SHINJI MASUDA. Signaling-state formation mechanism of a BLUF protein PapB from the purple bacterium Rhodopseudomonas palustris studied by femtosecond time-resolved absorption spectroscopy, Journal of Physical Chemistry B, Vol. 118, No. 51, pp. 14761-14773, 2014.  Official location  
• SHINJI MASUDA. Signaling-state formation mechanism of a BLUF protein PapB from the purple bacterium Rhodopseudomonas palustris studied by femtosecond time-resolved absorption spectroscopy., J. Phys. Chem. B 118: 14761-14773., 2014.
• Satoh, M., Tokaji, Y., Nagano, A.J., Hara-Nishimura, I., Hayashi, M., Nishimura, M., Ohta, H., Masuda, S.. Arabidopsis mutants affecting oxylipin signaling in photo-oxidative stress responses., Plant Physiol. Biochem., Vol. 81, pp. 90-95, Dec. 2013.
• Shimojima, M., Watanabe, T., Madoka, Y., Koizumi, R., Yamamoto, M. P., Masuda, K., Yamada, K., Masuda, S., Ohta, H.. Differential regulation of two types of monogalactosyldiacylglycerol synthase in membrane lipid remodeling under phosphate-limited conditions in sesame plants., Front. Plant Sci., Vol. 4, pp. 469, Nov. 2013.
• SHINJI MASUDA, Yuki Nakatani, Shukun Ren, Mikiko Tanaka. Blue light-mediated manipulation of transcription factor activity in vivo., ACS Chemical Biology, 8, 12, 2649-2653, Sept. 2013.
• Yuko Sasaki-Sekimoto, Yusuke Jikumaru, Takeshi Obayashi, Hikaru Saito, Shinji Masuda, Yuji Kamiya, Hiroyuki Ohta, Ken Shirasu. bHLH transcription factors JA-ASSOCIATED MYC2-LIKE 1, JAM2 and JAM3 are negative regulators of jasmonate responses in Arabidopsis., Plant physiology, July 2013.
• Shukun Ren, Ryoichi Sato, Koji Hasegawa, Hiroyuki Ohta, Shinji Masuda. A Predicted Structure for the PixD-PixE Complex Determined by Homology Modeling, Docking Simulations, and a Mutagenesis Study., Biochemistry, Vol. 52, 1272-1279, Feb. 2013.
• SHINJI MASUDA. Inhibition of Arabidopsis hypocotyl elongation by jasmonates is enhanced under red light in phytochrome B dependent manner., J. Plant Res. 126: 161-168., 2013.
• SHINJI MASUDA. Differential regulation of two types of monogalactosyldiacylglycerol synthase in membrane lipid remodeling under phosphate-limited conditions in sesame plants., Front. Plant Sci. 4: 469., 2013.
• Jing Chen, Kohei Sonobe, Narihito Ogawa, Shinji Masuda, Akira Nagatani, Yuichi Kobayashi, Hiroyuki Ohta. Inhibition of arabidopsis hypocotyl elongation by jasmonates is enhanced under red light in phytochrome B dependent manner, J. PLANT RES., Vol. 126, pp. 161-168, 2013.
• Ren, S., Sato, R., Hasegawa, K., Ohta, H., Masuda, S., SHINJI MASUDA. A predicted structure for the PixD-PixE complex determined by homology modeling, docking simulations, and a mutagenesis study, Biochemistry, Vol. 52, No. 7, pp. 1272-1279, 2013.  Official location  
• Sasaki-Sekimoto, Y., Jikumaru, Y., Obayashi, T., Saito, H., Masuda, S., Kamiya, Y., Ohta, H., Shirasu, K., SHINJI MASUDA. Basic helix-loop-helix transcription factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate responses in Arabidopsis, Plant Physiology, Vol. 163, No. 1, pp. 291-304, 2013.  Official location  
• Shimojima, M., Watanabe, T., Madoka, Y., Koizumi, R., Yamamoto, M.P., Masuda, K., Yamada, K., Masuda, S., Ohta, H., SHINJI MASUDA. Differential regulation of two types of monogalactosyldiacylglycerol synthase in membrane lipid remodeling under phosphate-limited conditions in sesame plants, Frontiers in Plant Science, Vol. 4, No. NOV, 2013.  Official location  
• SHINJI MASUDA. Blue light-mediated manipulation of transcription factor activity in vivo., ACS Chem. Biol. 8: 2649-2653., 2013.
• Masuda, S., Nakatani, Y., Ren, S., Tanaka, M., SHINJI MASUDA. Blue light-mediated manipulation of transcription factor activity in vivo, ACS Chemical Biology, Vol. 8, No. 12, pp. 2649-2653, 2013.  Official location  
• SHINJI MASUDA. Whole-genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum strain W4., Genome Announcements 1: e00577-13., 2013.
• Masuda, S., SHINJI MASUDA. Light detection and signal transduction in the BLUF photoreceptors, Plant and Cell Physiology, Vol. 54, No. 2, pp. 171-179, 2013.  Official location  
• SHINJI MASUDA. Basic helix-loop-helix transcription factors JASMONATE-ASSOCIATEDMYC2-LIKE1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate responses in Arabidopsis., Plant Physiol. 163: 291-304., 2013.
• SHINJI MASUDA. A predicted structure for the PixD-PixE complex determined by homology modeling, docking simulation, and a mutagenesis study., Biochemistry 52: 1272-1279., 2013.
• Chen, J., Sonobe, K., Ogawa, N., Masuda, S., Nagatani, A., Kobayashi, Y., Ohta, H., SHINJI MASUDA. Inhibition of arabidopsis hypocotyl elongation by jasmonates is enhanced under red light in phytochrome B dependent manner, Journal of Plant Research, Vol. 126, No. 1, pp. 161-168, 2013.  Official location  
• Awakawa, T., Sugai, Y., Otsutomo, K., Ren, S., Masuda, S., Katsuyama, Y., Horinouchi, S., Ohnishi, Y., SHINJI MASUDA. 4-Hydroxy-3-methyl-6-(1-methyl-2-oxoalkyl)pyran-2-one Synthesis by a Type III Polyketide Synthase from Rhodospirillum centenum, ChemBioChem, Vol. 14, No. 8, pp. 1006-1013, 2013.  Official location  
• SHINJI MASUDA. 4-hydroxy-3-methyl-6-(1-methyl-2-oxoalkyl)pyran-2-one synthesis by a type III polyketide synthase from Rhodospirillum centenum., ChemBioChem 14: 1006-1013., 2013.
• Yuichi Yuzawa, Hidenori Nishihara, Tsuyoshi Haraguchi, Shinji Masuda, Mie Shimojima, Atsushi Shimoyama, Hideya Yuasa, Norihiro Okada, Hiroyuki Ohta. Phylogeny of Galactolipid Synthase Homologs Together with Their Enzymatic Analyses Revealed A Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis, DNA Research, 19, (1), 91-102, Feb. 2012.
• Yuzawa, Y., Nishihara, H., Haraguchi, T., Masuda, S., Shimojima, M., Shimoyama, A., Yuasa, H., Okada, N., Ohta, H., SHINJI MASUDA. Phylogeny of galactolipid synthase homologs together with their enzymatic analyses revealed a possible origin and divergence time for photosynthetic membrane biogenesis, DNA Research, Vol. 19, No. 1, pp. 91-102, 2012.  Official location  
• SHINJI MASUDA. A PixD-PapB chimeric protein reveals the function of the BLUF domain C-terminal α-helices for light signal transduction., Plant Cell Physiol. 53: 1638-1647., 2012.
• Ren, S., Sawada, M., Hasegawa, K., Hayakawa, Y., Ohta, H., Masuda, S., SHINJI MASUDA. A PixD - PapB chimeric protein reveals the function of the BLUF domain C-terminal α-helices for light signal transduction, Plant and Cell Physiology, Vol. 53, No. 9, pp. 1638-1647, 2012.  Official location  
• Unno, M., Tsukiji, Y., Kubota, K., Masuda, S., SHINJI MASUDA. N-Terminal truncation does not affect the location of a conserved tryptophan in the BLUF domain of appa from rhodobacter sphaeroides, Journal of Physical Chemistry B, Vol. 116, No. 30, pp. 8974-8980, 2012.  Official location  
• SHINJI MASUDA. N-terminal truncation does not affect the location of a conserved tryptophan in the BLUF domain of AppA from Rhodobacter sphaeroides., J. Phys. Chem. B 116: 8974-8980., 2012.
• SHINJI MASUDA. Phylogeny of galactolipid synthase homologs together with their enzymatic analyses revealed a possible origin and divergence time for photosynthetic membrane biogenesis., DNA Res. 19: 91-102., 2012.
• SHINJI MASUDA, Harada, Jiro, Yokono, Makio, Yuichi Yuzawa, Mie Shimojima, Kazuhiro Murofushi, Hironori Tanaka, Hanako Masuda, Masato Murakawa, Haraguchi, Tsuyoshi, Kondo, Maki, Nishimura, Mikio, HIDEYA YUASA, Noguchi, Masato, Oh-oka, Hirozo, Tanaka, Ayumi, Tamiaki, Hitoshi, HIROYUKI OHTA. A Monogalactosyldiacylglycerol Synthase Found in the Green Sulfur Bacterium Chlorobaculum tepidum Reveals Important Roles for Galactolipids in Photosynthesis, Plant Cell, Vol. 23, No. 7, pp. 2644-2658, July 2011.  Official location  
• Kondo, T., Masuda, S., Tsutsui, K., Mino, H., SHINJI MASUDA. Temperature dependence of relaxation time of a stable radical pair in SyPixD investigated by pulsed EPR, Chemical Physics Letters, Vol. 501, No. 4-6, pp. 528-533, 2011.  Official location  
• Masuda, S., Harada, J., Yokono, M., Yuzawa, Y., Shimojima, M., Murofushi, K., Tanaka, H., Masuda, H., Murakawa, M., Haraguchi, T., Kondo, M., Nishimura, M., Yuasa, H., Noguchi, M., Oh-Oka, H., Tanaka, A., Tamiaki, H., Ohta, H., SHINJI MASUDA. A monogalactosyldiacylglycerol synthase found in the green sulfur bacterium Chlorobaculum tepidum reveals important roles for galactolipids in photosynthesis, Plant Cell, Vol. 23, No. 7, pp. 2644-2658, 2011.  Official location  
• SHINJI MASUDA. A monogalactosyldiacylglycerol synthase found in the green sulfur bacterium Chlorobaculum tepidum reveals important roles for galactolipids in photosynthesis., Plant Cell 23: 2644-2658., 2011.
• Kondo, T., Masuda, S., Mino, H., SHINJI MASUDA. Pulsed EPR Analysis of the Photo-Induced Triplet Radical Pair in the BLUF Protein SyPixD: Determination of the Protein-Protein Distance and Orientation in the Oligomeric Protein, Applied Magnetic Resonance, Vol. 40, No. 4, pp. 545-555, 2011.  Official location  
• SHINJI MASUDA. Pulsed ESR analysis of the photo-induced triplet radical pair in the BLUF protein SyPixD: Determination of the protein-protein distance and orientation in the oligomeric protein., Appl. Magn. Reson. 40: 545-555., 2011.
• SHINJI MASUDA. Temperature dependence of relaxation time of a stable radical pair in SyPixD investigated by pulsed EPR., Chem. Phys. Lett. 501: 528-533., 2011.
• Takafumi Narise, 小林康一, Mie Shimojima, SHINJI MASUDA, HIROYUKI OHTA. Involvement of auxin signaling mediated by IAA14 and ARF7/19 in membrane lipid remodeling during phosphate starvation., Plant Mol Biol., 72（4-5）, 533-44, Mar. 2010.
• SHINJI MASUDA. Structural refinement of a key tryptophan residue in the BLUF photoreceptor AppA by ultraviolet resonance Raman spectroscopy., Biophys. J. 98: 1949-1956., 2010.
• Unno, M., Kikuchi, S., Masuda, S., SHINJI MASUDA. Structural refinement of a key tryptophan residue in the BLUF photoreceptor AppA by ultraviolet resonance raman spectroscopy, Biophysical Journal, Vol. 98, No. 9, pp. 1949-1956, 2010.  Official location  
• SHINJI MASUDA. Temperature sensitive reaction of a photosensor protein YcgF: Possibility of a role of temperature sensor., Biochemistry 49: 2288-2296., 2010.
• Nakasone, Y., Ono, T.-A., Ishii, A., Masuda, S., Terazima, M., SHINJI MASUDA. Temperature-sensitive reaction of a photosensor protein YcgF: Possibility of a role of temperature sensor, Biochemistry, Vol. 49, No. 10, pp. 2288-2296, 2010.  Official location  
• Kanazawa, T., Ren, S., Maekawa, M., Hasegawa, K., Arisaka, F., Hyodo, M., Hayakawa, Y., Ohta, H., Masuda, S., SHINJI MASUDA. Biochemical and physiological characterization of a BLUF protein-EAL protein complex involved in blue light-dependent degradation of cyclic diguanylate in the purple bacterium rhodopseudomonas palustris, Biochemistry, Vol. 49, No. 50, pp. 10647-10655, 2010.  Official location  
• SHINJI MASUDA. Biochemical and physiological characterization of a BLUF protein-EAL protein complex involved in blue light-dependent degradation of cyclic diguanylate in the purple bacterium Rhodopseudomonas palustris., Biochemistry 49: 10647-10655., 2010.
• SHINJI MASUDA. Involvement of auxin signaling mediated by IAA14 and ARF7/19 in membrane lipid remodeling during phosphate starvation., Plant Mol. Biol. 72: 533-544., 2010.
• Narise, T., Kobayashi, K., Baba, S., Shimojima, M., Masuda, S., Fukaki, H., Ohta, H., SHINJI MASUDA. Involvement of auxin signaling mediated by IAA14 and ARF7/19 in membrane lipid remodeling during phosphate starvation, Plant Molecular Biology, Vol. 72, No. 4, pp. 533-544, 2010.  Official location  
• Masuda, S., Hasegawa, K., Ohta, H., Ono, T.. Crucial role in light signal transduction for the conserved Met93 of the BLUF protein PixD/Slr1694., Plant Cell Physiol. 49(10):1600-6., Vol. 49, No. 10, pp. 1600-1606, 2009.
• Masuda, S., Ikeda, R., Masuda, T., Hashimoto, H., Tsuchiya, T., Kojima, H., Nomata, J., Fujita, Y., Mimuro, M., Ohta, H., Takamiya, K.-I., SHINJI MASUDA. Prolamellar bodies formed by cyanobacterial protochlorophyllide oxidoreductase in Arabidopsis, Plant Journal, Vol. 58, No. 6, pp. 952-960, 2009.  Official location  
• SHINJI MASUDA. Prolamellar bodies formed by cyanobacterial protochlorophyllide oxidoreductase in Arabidopsis., Plant J. 58: 952-960., 2009.
• SHINJI MASUDA, Ikeda, R., TATSURU MASUDA, Hashimoto, H., Tsuchiya, T., Kojima, H., Nomata, J., Fujita, Y., Mimuro, M., HIROYUKI OHTA, KEN-ICHIRO TAKAMIYA. Prolamellar bodies formed by cyanobacterial protochlorophyllide oxidoreductase in Arabidopsis., Plant J., Vol. 58, pp. 952-960, 2009.
• Masuda, S., Tozawa, Y., Ohta, H., SHINJI MASUDA. Possible targets of "magic spots" in plant signalling, Plant Signaling and Behavior, Vol. 3, No. 11, pp. 1021-1023, 2008.  Official location  
• Mizusawa, K., Masuda, S., Ohta, H.. Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana., Planta, Vol. 228, pp. 553-562, 2008.
• Masuda, S., Tozawa, Y., Ohta, H.. Possible targets of “magic spots” in plant signaling., Plant Signaling Behavior., Vol. 3, pp. 1021-1023, 2008.
• Masuda, S., Hasegawa, K., Ohta, H., Ono, T.-A., SHINJI MASUDA. Crucial role in light signal transduction for the conserved Met93 of the BLUF protein PixD/Slr1694, Plant and Cell Physiology, Vol. 49, No. 10, pp. 1600-1606, 2008.  Official location  
• SHINJI MASUDA. Crucial role in light signal transduction for the conserved Met93 of the BLUF protein PixD/Slr1694., Plant Cell Physiol. 49: 1600-1606., 2008.
• Mizusawa, K., Masuda, S., Ohta, H., SHINJI MASUDA. Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana, Planta, Vol. 228, No. 4, pp. 553-562, 2008.  Official location  
• SHINJI MASUDA. Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana., Planta 228: 553-562., 2008.
• SHINJI MASUDA. Possible targets of “magic spots” in plant signaling., Plant Signaling Behavior 3: 1021-1023., 2008.
• Masuda, S., Berleman, J., Hasselbring, B.M., Bauer, C.E., SHINJI MASUDA. Regulation of aerobic photosystem synthesis in the purple bacterium Rhodospirillum centenum by CrtJ and AerR, Photochemical and Photobiological Sciences, Vol. 7, No. 10, pp. 1267-1272, 2008.  Official location  
• SHINJI MASUDA. Regulation of aerobic photosystem synthesis in the purple bacterium Rhodospirillum centenum., Photochem. Photobiol. Sci. 7: 1267-1272., 2008.
• Masuda, S., Mizusawa, K., Narisawa, T., Tozawa, Y., Ohta, H., Takamiya, K.-I., SHINJI MASUDA. The bacterial stringent response, conserved in chloroplasts, controls plant fertilization, Plant and Cell Physiology, Vol. 49, No. 2, pp. 135-141, 2008.  Official location  
• SHINJI MASUDA. The bacterial stringent response, conserved in chloroplasts, controls plant fertilization., Plant Cell Physiol. 49: 135-141., 2008.
• Masuda, S., Mizusawa, K., Narisawa, T., Tozawa, Y., Ohta, H., Takamiya, K.. The Bacterial Stringent Response, Conserved in Chloroplasts, Controls Plant Fertilization,, Plant Cell Physiol, Vol. 49, pp. 135-141, 2008.
• Wakita, M., Masuda, S., Motohashi, K., Hisabori, T., Ohta, H., Takamiya, K., Wakita, M., Motohashi, K., Hisabori, T, .Ohta, H., Takamiya, K.. The significance of Type II and PrxQ peroxiredoxins for antioxidative stress response in the purple bacterium Rhodobacter sphaeroides., J. Biol. Chem, Vol. 282, No. 38, pp. 27792-27801, Apr. 2007.  Official location  
• Nakasone, Y., Ono, T., Ishii, A., Masuda, S., Terazima, M.. Transient dimerization and conformational change of a BLUF protein: YcgF, J. Am. Chem. Soc., Vol. 129, pp. 7028-7035, 2007.
• Tozawa, Y., Nozawa, A., Kanno, T., Narisawa, T., Masuda, S., Kasai, K., Nanamiya, H.. Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants., J. Biol. Chem, Vol. 282, pp. 35536-35545, 2007.
• Hiroshi SHIMADA, Mochizuki, M., Ogura, K., Froehlich, J. E., Osteryoung, K. W., Shirano, Y., Shibata, D., Masuda, S., Mori, K., KEN-ICHIRO TAKAMIYA. Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase., Plant Cell, Vol. 19, pp. 3157-3169, 2007.
• Shimada, H., Mochizuki, M., Ogura, K., Froehlich, J.E., Osteryoung, K.W., Shirano, Y., Shibata, D., Masuda, S., Mori, K., Takamiya, K.-I., SHINJI MASUDA. Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase, Plant Cell, Vol. 19, No. 10, pp. 3157-3169, 2007.  Official location  
• SHINJI MASUDA. Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase., Plant Cell 19: 3157-3169., 2007.
• Tozawa, Y., Nozawa, A., Kanno, T., Narisawa, T., Masuda, S., Kasai, K., Nanamiya, H., SHINJI MASUDA. Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants, Journal of Biological Chemistry, Vol. 282, No. 49, pp. 35536-35545, 2007.  Official location  
• SHINJI MASUDA. Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants., J. Biol. Chem. 282: 35536-35545., 2007.
• SHINJI MASUDA. Purification and reconstitution of PYP-phytochrome with biliverdin and 4-hydroxycinnamic acid., Methods Enzymol. 422: 184-189., 2007.
• Masuda, S., Tomida, Y., Ohta, H., Takamiya, K.-i., SHINJI MASUDA. The Critical Role of a Hydrogen Bond between Gln63 and Trp104 in the Blue-Light Sensing BLUF Domain That Controls AppA Activity, Journal of Molecular Biology, Vol. 368, No. 5, pp. 1223-1230, 2007.  Official location  
• SHINJI MASUDA. The critical role of a hydrogen bond between Gln63 and Trp104 in the blue-light sensing BLUF domain that controls AppA activity., J. Mol. Biol. 368: 1223-1230., 2007.
• SHINJI MASUDA. Transient dimerization and conformational change of a BLUF protein: YcgF., J. Am. Chem. Soc. 129: 7028-7035., 2007.
• Nakasone, Y., Ono, T.-A., Ishii, A., Masuda, S., Terazima, M., SHINJI MASUDA. Transient dimerization and conformational change of a BLUF protein: YcgF, Journal of the American Chemical Society, Vol. 129, No. 22, pp. 7028-7035, 2007.  Official location  
• Chung, Y., Masuda, S., Bauer, C. E.. Purification and reconstitution of PYP-phytochrome with biliverdin and 4-hydroxycinnamic acid., Methods Enzymol, Vol. 422, pp. 184-189, 2007.
• Masuda, S., Tomida, Y., Ohta, H., Takamiya, K.. The critical role of a hydrogen bond between Gln63 and Trp104 in the blue-light sensing BLUF domain that controls AppA activity., J. Mol. Biol, Vol. 368, pp. 1223-1230, 2007.
• SHINJI MASUDA. A new membrane-bound cytochrome c works as an electron donor to the photosynthetic reaction center complex in the purple bacterium, Rhodovulum sulfidophilum., J. Biol. Chem. 282: 6463-6472., Vol. 282, No. 9, pp. 6463-6472, 2007.
• Unno, M., Masuda, S., Ono, T.-A., Yamauchi, S., SHINJI MASUDA. Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations, Journal of the American Chemical Society, Vol. 128, No. 17, pp. 5638-5639, 2006.  Official location  
• Yuan, H., Anderson, S., Masuda, S., Dragnea, V., Moffat, K., Bauer, C.. Crystal structure of the Synechocystis photoreceptor Slr1694 reveal distinct structural states related to signaling, Biochemistry, Vol. 45, pp. 12687-12694, 2006.
• Unno, M., Masuda, S., Ono, T., Yamauchi, S.. Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations., J. Am. Chem. Soc, Vol. 128, pp. 5638-5639, 2006.
• Hasegawa, K., Masuda, S., Ono, T.. Light-induced structural changes of a full-length protein and its BLUF domain in YcgF(BlrP), a blue-light sensing protein that uses FAD (BLUF)., Biochemistry, Vol. 45, pp. 3785-3793, 2006.
• SHINJI MASUDA. Light induced structural changes of a full-length protein and its BLUF domain in YcgF (Blrp), a blue-light sensing protein that uses FAD (BLUF)., Biochemistry 45, 3785-3793., 2006.
• Hasegawa, K., Masuda, S., Ono, T.-A., SHINJI MASUDA. Light induced structural changes of a full-length protein and its BLUF domain in YcgF(Blrp), a blue-light sensing protein that uses FAD (BLUF), Biochemistry, Vol. 45, No. 11, pp. 3785-3793, 2006.  Official location  
• Yuan, H., Anderson, S., Masuda, S., Dragnea, V., Moffat, K., Bauer, C., SHINJI MASUDA. Crystal structures of the Synechocystis photoreceptor Slr1694 reveal distinct structural states related to signaling, Biochemistry, Vol. 45, No. 42, pp. 12687-12694, 2006.  Official location  
• SHINJI MASUDA. Crystal structures of the Synechocystis photoreceptor Slr1694 reveal distinct structural states related to signaling., Biochemistry 45, 12687-12694., 2006.
• SHINJI MASUDA. Orientation of a key Glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations., J. Am. Chem. Soc. 128, 5638-5639., 2006.
• Makihara, F., Tsuzuki, M., Sato, K., Masuda, S., Nagashima, K.V.P., Abo, M., Okubo, A., SHINJI MASUDA. Role of trehalose synthesis pathways in salt tolerance mechanism of Rhodobacter sphaeroides f. sp. denitrificans IL106, Archives of Microbiology, Vol. 184, No. 1, pp. 56-65, 2005.  Official location  
• Masuda, S., Hasegawa, K., Ono, T.. Adenosine diphosphate moiety does not participate in structural changes for the signaling state in the sensor of blue-light using FAD domain of AppA., FEBS Lett., Vol. 579, pp. 4329-4332, 2005.
• Masuda, S., Ono, T.. Adenylyl cycles activity of Cya1 from the cyanobacterium Synechocystis sp. PCC 6803 is inhibited by bicarbonate., J. Bacteriol., Vol. 187, pp. 5032-5035, 2005.
• Unno, M., Sano, R., Masuda, S., Ono, T., Yamauchi, S.. Light-induced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy., J. Phys. Chem. B, Vol. 109, pp. 12620-12626, 2005.
• Anderson, S., Dragnea, V., Masuda, S., Ybe, J., Moffat, K., Bauer, C. E.. Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides., Biochemistry, Vol. 44, pp. 7998-8005, 2005.
• Masuda, S., Hasegawa, K., Ono, T.-A., SHINJI MASUDA. Adenosine diphosphate moiety does not participate in structural changes for the signaling state in the sensor of blue-light using FAD domain of AppA, FEBS Letters, Vol. 579, No. 20, pp. 4329-4332, 2005.  Official location  
• SHINJI MASUDA. Adenosine diphosphate moiety does not participate in structural changes for the signaling state in the sensor of blue-light using FAD domain of AppA., FEBS Lett. 579, 4329-4332., 2005.
• Masuda, S., Ono, T.-A., SHINJI MASUDA. Adenylyl cyclase activity of Cya1 from the cyanobacterium synechocystis sp. strain PCC 6803 is inhibited by bicarbonate, Journal of Bacteriology, Vol. 187, No. 14, pp. 5032-5035, 2005.  Official location  
• SHINJI MASUDA. Adenylyl cycles activity of Cya1 from the cyanobacterium Synechocystis sp. PCC 6803 is inhibited by bicarbonate., J. Bacteriol. 187, 5032-5035., 2005.
• Unno, M., Sano, R., Masuda, S., Ono, T.-A., Yamauchi, S., SHINJI MASUDA. Light-induced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy, Journal of Physical Chemistry B, Vol. 109, No. 25, pp. 12620-12626, 2005.  Official location  
• SHINJI MASUDA. Light-induced structural changes in the active site of the BLUF domain in AppA by Raman spectroscopy., J. Phys. Chem. B 109, 12620-12626., 2005.
• Masuda, S., Hasegawa, K., Ono, T.-A., SHINJI MASUDA. Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state, Biochemistry, Vol. 44, No. 4, pp. 1215-1224, 2005.  Official location  
• SHINJI MASUDA. Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state., Biochemistry 44, 1215-1224., 2005.
• Hasegawa, K., Masuda, S., Ono, T.-A., SHINJI MASUDA. Spectroscopic analysis of the dark relaxation process of a photocycle in a sensor of blue light using FAD (BLUF) protein Slr1694 of the cyanobacterium Synechocystis sp. PCC6803, Plant and Cell Physiology, Vol. 46, No. 1, pp. 136-146, 2005.  Official location  
• SHINJI MASUDA. Spectroscopic analysis of the dark relaxation process of a photocycle in a sensor of blue-light using FAD (BLUF) protein Slr1694 of cyanobacterium Synechocystis sp. PCC 6803., Plant Cell Physiol. 46, 136-146., 2005.
• Anderson, S., Dragnea, V., Masuda, S., Ybe, J., Moffat, K., Bauer, C., SHINJI MASUDA. Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides, Biochemistry, Vol. 44, No. 22, pp. 7998-8005, 2005.  Official location  
• SHINJI MASUDA. Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides., Biochemistry 44, 7998-8005., 2005.
• SHINJI MASUDA. Triptophan at position 104 is involved in transforming light signal into changes of β-sheet structure for the signaling state in the BLUF domain of AppA., Plant Cell Physiol. 46, 1894-1901., 2005.
• Masuda, S., Hasegawa, K., Ono, T.-A., SHINJI MASUDA. Tryptophan at position 104 is involved in transforming light signal into changes of β-sheet structure for the signaling state in the BLUF domain of AppA, Plant and Cell Physiology, Vol. 46, No. 12, pp. 1894-1901, 2005.  Official location  
• Masuda, S., Hasegawa, K., Ono, T.. Tryptophan at position 104 is involved in transforming light signal into changes of beta-sheet structure for the signalling state in the BLUF domain of AppA, Plant Cell Physiol, Vol. 46, pp. 1894-1901, 2005.
• Masuda, S., Hasegawa, K., Ono, T.. Light-induced structural changes of apoprotein and chromophore in the sensor of blue light using FAD (BLUF) domain of AppA for a signaling state., Biochemistry, Vol. 44, pp. 1215-1224, 2005.
• Hasegawa, K., Masuda, S., Ono, T.. Spectroscopic analysis of the dark relaxation process of a photocycle in a sensor of blue-light using FAD (BLUF) protein Slr1694 of cyanobacterium Synechocystis sp. PCC 6803., Plant Cell Physiol., Vol. 46, pp. 136-146, 2005.
• Masuda, S., Ono, T.-A., SHINJI MASUDA. Biochemical characterization of the major adenylyl cyclase, Cya1, in the cyanobacterium Synechocystis sp. PCC 6803, FEBS Letters, Vol. 577, No. 1-2, pp. 255-258, 2004.  Official location  
• Masuda, S., Hasegawa, K., Ishii, A., Ono, T.. Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of Synechocystis sp. PCC6803., Biochemistry, Vol. 43, pp. 5304-5313, 2004.
• SHINJI MASUDA. Structural intermediate in the photocycle of a BLUF (sensor of blue-light using FAD) protein Slr1694 in a cyanobacterium Synechocystis sp. PCC 6803., Biochemistry 43, 14979-14986., 2004.
• Hasegawa, K., Masuda, S., Ono, T.-A., SHINJI MASUDA. Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a cyanobacterium Synechocystis sp. PCC6803, Biochemistry, Vol. 43, No. 47, pp. 14979-14986, 2004.  Official location  
• Tsukatani, Y., Matsuura, K., Masuda, S., Shimada, K., Hiraishi, A., Nagashima, K.V.P., SHINJI MASUDA. Phylogenetic distribution of unusual triheme to tetraheme cytochrome subunit in the reaction center complex of purple photosynthetic bacteria, Photosynthesis Research, Vol. 79, No. 1, pp. 83-91, 2004.  Official location  
• Masuda, S., Ono, T.. Biochemical characterization of the major adenylyl cyclase, Cya1, in the cyanobacterium Synechocystis sp. PCC 6803., FEBS Lett., Vol. 577, pp. 255-258, 2004.
• Masuda, S., Hasegawa, K., Ishii, A., Ono, T.-A., SHINJI MASUDA. Light-Induced Structural Changes in a Putative Blue-Light Receptor with a Novel FAD Binding Fold Sensor of Blue-Light Using FAD (BLUF); Slr1694 of Synechocystis sp. PCC6803, Biochemistry, Vol. 43, No. 18, pp. 5304-5313, 2004.  Official location  
• SHINJI MASUDA. Phylogenetic distribution of unusual triheme to tetraheme cytochrome subunit in the reaction center complex of purple bacteria., Photosynth. Res. 79: 83-91., 2004.
• SHINJI MASUDA. Biochemical characterization of the major adenylyl cyclase, Cya1, in a cyanobacterium Synechocystis sp. PCC 6803., FEBS Lett. 577, 255-258., 2004.
• SHINJI MASUDA. Null mutation of HvrA compensates for loss of an essential relA/spoT-like gene in Rhodobacter capsulatus., J. Bacteriol. 186: 235-239., 2004.
• Hasegawa, K., Masuda, S., Ono, T.. Structural intermediate in the photocycle of a BLUF (sensor of blue light using FAD) protein Slr1694 in a Cyanobacterium Synechocystis sp. PCC6803, Biochemistry, Vol. 43, pp. 14979-14986, 2004.
• SHINJI MASUDA. Light-induced structural changes in a putative blue-light receptor with a novel FAD binding fold sensor of blue-light using FAD (BLUF); Slr1694 of Synechocystis sp. PCC6803., Biochemistry 43: 5304-5313., 2004.
• Masuda, S., Bauer, C.E., SHINJI MASUDA. Null Mutation of HvrA Compensates for Loss of an Essential relA/spoT-Like Gene in Rhodobacter capsulatus, Journal of Bacteriology, Vol. 186, No. 1, pp. 235-239, 2004.  Official location  
• Tsukatani, Y., Matsuura, K., Masuda S., Shimada, K., Hiraishi, A., Nagashima, K.V.P.. Phylogenetic distribution of unusual triheme to tetraheme cytochrome subunit in the reaction center complex of purple bacteria., Photosynth. Res., Vol. 79, pp. 83-91, 2004.
• Masuda, S., Bauer C. E.. Null mutation of HvrA compensates for loss of an essential relA/spoT-like gene in Rhodobacter capsulatus., J. Bacteriol., Vol. 186, pp. 235-239, 2004.
• Bauer, C.E., Elsen, S., Swem, L.R., Swem, D.L., Masuda, S.. Redox and light regulation of gene expression in photosynthetic prokaryotes., Philos. Trans. R. Soc. Lond. B. Biol. Sci., Vol. 358, pp. 147-154, 2003.
• SHINJI MASUDA. Spectroscopic and mutational analysis of the blue-light photoreceptor AppA: A novel photocycle involving flavin stacking with an aromatic amino acid., Biochemisty 42: 6726-6734., 2003.
• Kraft, B. J., Masuda, S., Kikuchi, J., Dragnea, V., Tollin, G., Zaleski, J. M., Bauer, C. E.. Spectroscopic and mutational analysis of the blue-light photoreceptor AppA: A novel photocycle involving flavin stacking with an aromatic amino acid., Biochemistry, Vol. 42, pp. 6726-6734, 2003.
• Swem, L. R., Kraft, B. J., Swem, D. L., Setterdahl, A. T., Masuda, S., Knaff, D. B., Zaleski, J. M., Bauer C. E.. Signal transduction by the global regulator RegB is mediated by a redox-active cysteine., EMBO J., Vol. 22, pp. 4699-4708, 2003.
• Kraft, B.J., Masuda, S., Kikuchi, J., Dragnea, V., Tollin, G., Zaleski, J.M., Bauer, C.E., SHINJI MASUDA. Spectroscopic and mutational analysis of the blue-light photoreceptor AppA: A novel photocycle involving flavin stacking with an aromatic amino acid, Biochemistry, Vol. 42, No. 22, pp. 6726-6734, 2003.  Official location  
• SHINJI MASUDA. Signal transduction by the global regulator RegB is mediated by a redox-active cysteine., EMBO J. 22: 4699-4708., 2003.
• Bauer, C., Elsen, S., Swem, L.R., Swem, D.L., Masuda, S., Blankenship, R.E., Allen, J.F., Martin, W., SHINJI MASUDA. Redox and light regulation of gene expression in photosynthetic prokaryotes, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 358, No. 1429, pp. 147-154, 2003.  Official location  
• Swem, L.R., Kraft, B.J., Swem, D.L., Setterdahl, A.T., Masuda, S., Knaff, D.B., Zaleski, J.M., Bauer, C.E., SHINJI MASUDA. Signal transduction by the global regulator RegB is mediated by a redox-active cysteine, EMBO Journal, Vol. 22, No. 18, pp. 4699-4708, 2003.  Official location  
• Masuda, S., Dong, C., Swem, D., Setterdahl, A.T., Knaff, D., Bauer C.E.. Repression of photosynthesis gene expression by formation of a disulfide bond in CrtJ., Proc. Natl. Acad. Sci. USA., Vol. 99, pp. 7078-7083, 2002.
• SHINJI MASUDA. Mutational analyses of the photosynthetic reaction-center-bound triheme cytochrome subunit and cytochrome c2 in the purple bacterium, Rhodovulum sulfidophilum., Biochemistry 41: 11211-11217., 2002.
• Masuda, S., Dong, C., Swem, D., Setterdahl, A.T., Knaff, D.B., Bauer, C.E., SHINJI MASUDA. Repression of photosynthesis gene expression by formation of a disulfide bond in CrtJ, Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 10, pp. 7078-7083, 2002.  Official location  
• SHINJI MASUDA. Repression of photosynthesis gene expression by formation of a disulfide bond in CrtJ., Proc. Natl. Acad. Sci. USA. 99: 7078-7083., 2002.
• Masuda, S., Bauer, C.E.. AppA is a blue-light photoreceptor that anti-represses photosynthesis gene expression in Rhodobacter sphaeroides., Cell, Vol. 110, pp. 613-623, 2002.
• Masuda, S., Tsukatani, Y., Kimura, Y., Nagashima, K.V.P., Shimada, K., Matsuura, K.. Mutational analyses of the photosynthetic reaction-center-bound triheme cytochrome subunit and cytochrome c2 in the purple bacterium, Rhodovulum sulfidophilum., Biochemistry, Vol. 41, pp. 11211-11217, 2002.
• Masuda, S., Tsukatani, Y., Kimura, Y., Nagashima, K.V.P., Shimada, K., Matsuura, K., SHINJI MASUDA. Mutational analyses of the photosynthetic reaction center-bound triheme cytochrome subunit and cytochrome c2 in the purple bacterium Rhodovulum sulfidophilum, Biochemistry, Vol. 41, No. 37, pp. 11211-11217, 2002.  Official location  
• Masuda, S., Bauer, C.E., SHINJI MASUDA. AppA is a blue light photoreceptor that antirepresses photosynthesis gene expression in Rhodobacter sphaeroides, Cell, Vol. 110, No. 5, pp. 613-623, 2002.  Official location  
• SHINJI MASUDA. AppA is a blue-light photoreceptor that anti-represses photosynthesis gene expression in Rhodobacter sphaeroides., Cell 110: 613-623., 2002.
• SHINJI MASUDA. In vitro and in vivo electron transfer to the triheme cytochrome subunit bound to the photosynthetic reaction center complex in the purple bacterium Rhodovulum sulfidophilum., Biochim. Biophy. Acta 1506: 23-30., 2001.
• Yoshida, M., Masuda, S., Nagashima, K.V.P., Vermeglio, A., Shimada, K., Matsuura, K.. In vitro and in vivo electron transfer to the triheme cytochrome subunit bound to the photosynthetic reaction center complex in the purple bacterium Rhodovulum sulfidophilum., Biochim. Biophy. Acta, Vol. 1506, pp. 23-30, 2001.
• Yoshida, M., Masuda, S., Nagashima, K.V.P., Verméglio, A., Shimada, K., Matsuura, K., SHINJI MASUDA. In vitro and in vivo electron transfer to the triheme cytochrome subunit bound to the photosynthetic reaction center complex in the purple bacterium Rhodovulum sulfidophilum, Biochimica et Biophysica Acta - Bioenergetics, Vol. 1506, No. 1, pp. 23-30, 2001.  Official location  
• SHINJI MASUDA. Transcriptional control of expression of genes for photosynthetic reaction center and light-harvesting proteins in the purple bacterium Rhodovulum sulfidophilum., J. Bacteriol. 182: 2778-2786., 2000.
• Masuda, S., Nagashima, K.V.P., Shimada, K., Matsuura, K.. Transcriptional control of expression of genes for photosynthetic reaction center and light-harvesting proteins in the purple bacterium Rhodovulum sulfidophilum., J. Bacteriol., Vol. 182, pp. 2778-2786, 2000.
• Masuda, S., Nagashima, K.V.P., Shimada, K., Matsuura, K., SHINJI MASUDA. Transcriptional control of expression of genes for photosynthetic reaction center and light-harvesting proteins in the purple bacterium Rhodovulum sulfidophilum, Journal of Bacteriology, Vol. 182, No. 10, pp. 2778-2786, 2000.  Official location  
• SHINJI MASUDA. Structural and functional analyses of photosynthetic regulatory genes regA and regB from Rhodovulum sulfidophilum, Roseobacter denitrificans, and Rhodobacter capsulatus., J. Bacteriol. 181: 4205-4215., 1999.
• SHINJI MASUDA. A new cytochrome subunit bound to the photosynthetic reaction center in the purple bacterium, Rhodovulum sulfidophilum., J. Biol. Chem. 274: 10795-10801., 1999.
• Masuda, S., Yoshida, M., Nagashima, K.V.P., Shimada, K., Matsuura, K., SHINJI MASUDA. A new cytochrome subunit bound to the photosynthetic reaction center in the purple bacterium, Rhodovulum sulfidophilum, Journal of Biological Chemistry, Vol. 274, No. 16, pp. 10795-10801, 1999.  Official location  
• Masuda, S., Matsumoto, Y., Nagashima, K.V.P., Shimada, K., Inoue, K., Bauer, C.E., Matsuura, K.. Structural and functional analyses of photosynthetic regulatory genes regA and regB from Rhodovulum sulfidophilum, Roseobacter denitrificans, and Rhodobacter capsulatus., J. Bacteriol., Vol. 181, pp. 4205-4215, 1999.
• Masuda, S., Yoshida, M., Nagashima, K.V.P., Shimada, K., Matsuura, K.. A new cytochrome subunit bound to the photosynthetic reaction center in the purple bacterium, Rhodovulum sulfidophilum., J. Biol. Chem., Vol. 274, pp. 10795-10801, 1999.
• Masuda, S., Matsumoto, Y., Nagashima, K.V.P., Shimada, K., Inoue, K., Bauer, C.E., Matsuura, K., SHINJI MASUDA. Structural and functional analyses of photosynthetic regulatory genes regA and regB from Rhodovulum sulfidophilum, Roseobacter denitrificans, and Rhodobacter capsulatus, Journal of Bacteriology, Vol. 181, No. 14, pp. 4205-4215, 1999.  Official location  
• Oshima, T., Aiba, H., Baba, T., Fujita, K., Hayashi, K., Honjo, A., Ikemoto, K., Inada, T., Itoh, T., Kajihara, M., Kanai, K., Kashimoto, K., Kimura, S., Kitagawa, M., Makino, K., Masuda, S., Miki, T., Mizobuchi, K., Mori, H., Motomura, K., Nakamura, Y., Nashimoto, H., Nishio, Y., Saito, N., Horiuchi, T., SHINJI MASUDA. A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map (supplement)., DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 3, No. 3, pp. 211-223, 1996.  Official location  
• Oshima, T., Aiba, H., Baba, T., Fujita, K., Hayashi, K., Honjo, A., Ikemoto, K., Inada, T., Itoh, T., Kajihara, M., Kanai, K., Kashimoto, K., Kimura, S., Kitagawa, M., Makino, K., Masuda, S., Miki, T., Mizobuchi, K., Mori, H., Motomura, K., Nakamura, Y., Nashimoto, H., Nishio, Y., Saito, N., Horiuchi, T., SHINJI MASUDA. A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map (supplement)., DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 3, No. 3, pp. 211-223, 1996.  Official location  

Book

• Masuda, S., Tanaka, M., SHINJI MASUDA. PICCORO: A technique for manipulating the activity of transcription factors with blue light, Methods in Cell Biology, 2016.  Official location  
• Mashuda,S., Ohta,H.. バイオ系のための基礎科学問題集, 講談社サイエンティフィック, pp. I-13章 光合成 P48-50, 2007.
• Chung, Y., Masuda, S., Bauer, C.E., SHINJI MASUDA. Purification and Reconstitution of PYP-Phytochrome with Biliverdin and 4-Hydroxycinnamic Acid, Methods in Enzymology, Vol. 422, pp. 184-189, 2007.  Official location  
• Shinji Masuda, Taka-aki Ono. Comparative spectroscopic studies of sensor of blue-light using FAD (BLUF) proteins, AppA of Rhodobacter sphaeroides and YcgF of Escherichia coli., Photosynthesis: Fundamental aspects to global perspectives (van der Est and Bruce, D. Edts) Allen Press, Vol. 2, pp. 700-702, 2005.
• Masuda, S., Bauer, C.E., SHINJI MASUDA. The Antirepressor AppA Uses the Novel Flavin-Binding BLUF Domain as a Blue-Light-Absorbing Photoreceptor to Control Photosystem Synthesis, Handbook of Photosensory Receptors, pp. 433-445, 2005.  Official location  
• Shinji Masuda, Carl E. Bauer. The antirepressor AppA uses the novel flavin-binding BLUF domain as blue-light-absorbing photoreceptor to control photosystem synthesis., Handbook of Photosensory Receptors (Briggs, W. R., and Spudich, J., Eds.) Wiley-VCH Verlag GmbH, pp. 433-445., 2005.
• Masuda, S., Matsumoto, Y., Nagashima, K.V.P., Shimada, K., Inoue, K., Bauer, C.E., Matsuura, K.. Characterization of photosynthetic regulatory genes, regA and regB: Studies among different species, Photosynthesis: Mechanisms and Effects (Garab, G., ed.). Kluwer Academic Publishers, Photosynthesis: Mechanisms and Effects (Garab, G., ed.). Kluwer Academic Publishers, pp. 2881-2884, 1998.

International Conference (Reviewed)

• Unno, M., Kikuchi, S., Masuda, S., SHINJI MASUDA. Structural refinement of a key tryptophan residue in the BLUF photoreceptor AppA by ultraviolet resonance Raman spectroscopy, AIP Conference Proceedings, Vol. 1267, pp. 623-624, 2010.  Official location  

International Conference (Not reviewed / Unknown)

• SHINJI MASUDA. Physiological and genetic characterization of a gene for the stringent response in Chlamydomonas reinharditii, Nov. 2018.
• SHINJI MASUDA. Fluctuating-Light-Acclimation Protein 1 (FLAP1): Genetic-based characterization of a new factor contributing to proton gradient regulation across Arabidopsis thylakoid membranes, Nov. 2018.
• SHINJI MASUDA. Glycolipid and chlorophyll a biosynthesis are required for heterologous assembly of the type-I photochemical reaction center in purple bacteria, Aug. 2018.
• SHINJI MASUDA. Role of a new gene for the stringent response in Chlamydomonas reinharditii, Aug. 2018.
• SHINJI MASUDA. Impact of the stringent response for controlling photosynthesis and chloroplast function in photosynthetic microorganisms, Aug. 2018.
• SHINJI MASUDA. Glycolipid and chlorophyll a biosynthesis are required for heterologous assembly of the type-I photochemical reaction center in purple bacteria, Aug. 2018.
• SHINJI MASUDA. Intracellular signaling by PixD and PixE controlling phototaxis in the cyanobacterium Synechocystis sp. PCC6803, Aug. 2018.
• SHINJI MASUDA. Persulfide-responsive transcriptional repressor SqrR regulates sulfide-dependent photosynthesis, 2018.
• SHINJI MASUDA. Significance of light-induced electron transfer between a flavin molecule and an amino-acid side chain for controlling phototaxis in cyanobacteria, The 4th Awaji International Workshop on Electron Spin Science & Technology, 2016.
• SHINJI MASUDA. BLUF: the highly conserved blue-light photoreceptor controlling a wide variety of physiological activities in microorganisms, 環境微生物系学会合同大会2014シンポジウム「Marvelous strategy for bacterial survival」, 2016.
• SHINJI MASUDA. Significance of dynamic interaction between the BLUF photoreceptor PixD and its downstream factor PixE for controlling phototaxis in cyanobacteria, The International Chemical Congress of Pacific Basin Societies, Dec. 2015.
• Shinji Masuda. Molecular mechanisms of blue-light sensing by BLUF photoreceptors, 岡崎統合バイオサイエンスセンター サマースクール2015, Aug. 2015.
• Shinji Masuda, Yuki Nakatani, Shukun Ren, Mikiko Tanaka. “PICCORO”-a novel technique for manipulating the activity of transcription factors with blue light., 6th Strategic Conference of Zebrafish Investigators, Jan. 2015.

Domestic Conference (Not reviewed / Unknown)

• Yusuke Hori, Tatsuhiro Horii, SHINJI MASUDA, Toshinori Fujie. 植物葉面に貼付可能な透明超薄膜電極の開発と生体電位応答の計測, 第85回応用物理学会秋季学術講演会, Sept. 2024.
• SHINJI MASUDA. 緑色硫黄細菌の光合成反応中心コアアンテナ系におけるカロテノイド配糖体エステルによる超高速消光, Jan. 2019.

Other Publication

• SHINJI MASUDA. The Stringent Response in Phototrophs, ADVANCES IN PHOTOSYNTHESIS - FUNDAMENTAL ASPECTS, INTECH EUROPE, pp. 487-500, 2012.
• SHINJI MASUDA. 光合成細菌の光に依存したバイオフィルム形成機構, バイオサイエンスとインダストリー = Bioscience & industry, Vol. 69, No. 3, pp. 213-214, May 2011.
• SHINJI MASUDA. 2SA-04 What should we learn from BLUF proteins? : Light perception and signal transduction(2SA Photobiophysics promoted by young scientists,The 49th Annual Meeting of the Biophysical Society of Japan), 生物物理, 一般社団法人 日本生物物理学会, Vol. 51, pp. S14, 2011.
• SHINJI MASUDA. 被子植物のプラスチドで形成されるプロラメラボディに関する新知見, 生物物理, The Biophysical Society of Japan General Incorporated Association, Vol. 50, No. 1, pp. 36-37, Jan. 2010.
• Shinji Masuda. Functional Implications and Photocycle Mechanisms of BLUF Proteins, 生物物理, Vol. 45, pp. 308-313, 2005.

Patent

• SHINJI MASUDA. ｐｐＧｐｐ富化生物の製造方法及び生物. Patent. Published. 国立大学法人東京工業大学, 日本電信電話株式会社. 2022/04/19. 特願2022-069028. 2023/10/31. 特開2023-158948. 2023.
• SHINJI MASUDA, Takayuki Shimizu. 活性イオウ分子種に応答して遺伝子発現を制御するタンパク質. Patent. Published. 国立大学法人東京工業大学. 2017/01/31. 特願2017-015348. 2018/08/09. 特開2018-121557. 2018.
• SHINJI MASUDA, Mikiko Tanaka, Yuki Nakatani. 転写因子の機能制御方法. Patent. Published. 国立大学法人東京工業大学. 2012/05/23. 特願2012-117619. 2013/12/09. 特開2013-243940. 2013. Dec.
• SHINJI MASUDA. 貧栄養耐性植物の作出方法. Patent. Published. 国立大学法人東京工業大学. 2011/03/07. 特願2011-049320. 2012/09/27. 特開2012-183040. 2012.

Degree

• Structure and oxygen regulation of photosynthesis genes in purple bacteria,  Thesis,  Doctor of Science,  Tokyo Metropolitan University,  2000/--/--, 

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