研究成果

計画研究

田口 英樹（東京工業大学・科学技術創成研究院・細胞制御工学研究センター　教授）

  1. Miwa T, *Taguchi, H. Escherichia coli small heat shock protein IbpA plays a role in regulating the heat shock response by controlling the translation of σ32. Proc Natl Acad Sci USA, 120:e2304841120 (2023).
  2. *Chiba S, Fujiwara K, Chadani Y, *Taguchi H. Nascent chain-mediated translation regulation in bacteria: translation arrest and intrinsic ribosome destabilization. (review) J Biochem 173, 227–236 (2023). (J Biochem Special Issue)
  3. Yamakawa A, *Niwa T, *Chadani Y, Akinao Kobo, *Taguchi H. A method to enrich polypeptidyl-tRNAs to capture snapshots of translation in the cell. Nucleic Acids Res 51, e30 (2023).
  4. Minami S, Niwa T, Uemura E, Koike R, Taguchi H, *Ota M. A method that predicts chaperonin GroE substrates using small structural patterns of proteins. FEBS Open Bio 13, 779–794 (2023).
  5. Ito Y, *Chadani Y, Niwa T, Yamakawa A, Machida K, Imataka H, *Taguchi H. Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes. Nat Commun 13, 7451 (2022).
  6. Nakagawa Y, Shen HC-H, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, *Taguchi H, *Tanaka M. Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. Nat Chem Biol 18, 321–331 (2022).
  7. *Chadani Y, Sugata N, Niwa T, Ito Y, Iwasaki S, *Taguchi H. Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation. EMBO J 40, e108299 (2021).
  8. Miwa T, Chadani Y, *Taguchi H. Escherichia coli small heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at post-transcriptional levels. Mol Microbiol 115, 142–156 (2021).
  9. Miwa T, *Taguchi H. Novel self-regulation strategy of a small heat shock protein for prodigious and rapid expression on demand. 【Review】. Current Genetics (2021) in press
  10. Konno H, Watanabe-Nakayama T, Uchihashi T, Okuda M, Zhu L, Noriyuki Kodera, Kikuchi Y, *Ando T, *Taguchi H. Dynamics of oligomer and amyloid fibril formation by yeast prion Sup35 observed by high-speed atomic force microscopy. Proc Natl Acad Sci USA 117, 7831-7836 (2020)
  11. Muta M, *Iizuka R, Niwa T, Guo Y, Taguchi H and *Funatsu T. Nascent SecM chain interacts with outer ribosomal surface to stabilize translation arrest. Biochem J. 477, 557-566 (2020)

千葉 志信（京都産業大学・生命科学部　教授）

  1. Shiota N, Shimokawa-Chiba N, Fujiwara K, *Chiba S. Identification of Bacillus subtilis YidC substrates using a MifM-instructed translation arrest-based reporter. J Mol Biol, in press (2023).
  2. *Chiba S, Fujiwara K, Chadani Y, *Taguchi H. Nascent chain-mediated translation regulation in bacteria: translation arrest and intrinsic ribosome destabilization. (review) J Biochem 173, 227–236 (2023). (J Biochem Special Issue)
  3. Sakiyama K, Shimokawa-Chiba N, Fujiwara K and Chiba S. Search for translation arrest peptides encoded upstream of genes for components of protein localization pathways. Nucleic Acids Res. 49, 1550-1566 (2021) doi: 10.1093/nar/gkab024.
  4. Fujiwara K, Katagi Y, Ito K and Chiba S. Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter. Cell Rep. 33, 108250 (2020) doi: 10.1016/j.celrep.2020.108250.

内藤 哲（北海道大学大学院・農学研究院　研究院）

  1. Hiragori Y, Takahashi H, Karino T, Kaido A, Hayashi N, Sasaki S, Nakao K, Motomura T, Yamashita Y, Naito S, *Onouchi H. Genome-wide identification of Arabidopsis non-AUG initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels. Plant Mol Biol 111, 37–55 (2023).
  2. *Sotta N, Chiba Y, Aoyama H, Takamatsu S, Suzuku T, Miwa K, Yamashita Y, *Naito S, *Fujiwara T. Translational landscape of a C4 plant Sorghum bicolor, under normal and sulfur-deficient conditions. Plant Cell Physiol 63, 592–604 (2022).
  3. *Sotta N, Chiba Y, Miwa K, Takamatsu S, Tanaka M, Yamashita Y, *Naito S, *Fujiwara T. Global analysis of boron-induced ribosome stalling reveals its effects on translation termination and unique regulation by AUG-stops in Arabidopsis shoots. Plant J. (2021) in press doi: 10.1111/tpj.2021.15248
  4. Takamatsu S, Ohashi Y, Onoue N, Tajima Y, Imamichi T, Yonezawa S, Morimoto K, Onouchi H, Yamashita Y and Naito S. Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction. Nucleic Acids Res. 48, 1985-1999 (2020)
  5. *Takahashi H, Miyaki S, Onouchi H, Motomura T, Idesako N, Takahashi A, Murase M, Fukuyoshi S, Endo T, Satou K, Naito S, *Itoh M. Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes. Sci. Rep. 10, 16289 (2020). doi: 10.1038/s41598-020-73307-6
  6. *Takahashi H, Hayashi N, Hiragori Y, Sasaki S, Motomura T, Yamashita Y, Naito S, Takahashi A, Fuse K, Satou K, Endo T, Kojima S, *Onouchi H. Comprehensive genomewide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA. BMC Genomics 21, 260 (2020) doi: 10.1186/s12864-020-6662-5

永井 義隆（近畿大学・医学部・脳神経内科　教授）

  1. Fujino Y, Ueyama M, Ishiguro T, Ozawa D, Sugiki T, Ito H, Murata A, Ishiguro A, Gendron TF, Mori K, Tokuda E, Taminato T, Konno T, Koyama A, Kawabe Y, Takeuchi T, Furukawa Y, Fujiwara T, Ikeda M, Mizuno T, Mochizuki H, Mizusawa H, Wada K, Ishikawa K, Onodera O, Nakatani K, Taguchi H, Petrucelli L, *Nagai Y. FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD. eLife 12, RP84338 (2023).
  2. Taminato T, *Takeuchi T, Ueyama M, Mori K, Ikeda M, Mochizuki H, *Nagai Y. Therapeutic reduction of GGGGCC repeat RNA levels by hnRNPA3 suppresses neurodegeneration in Drosophila models of C9orf72-linked ALS/FTD. Hum Mol Genet 32, 1673–1682 (2023).
  3. Fujino Y, Mori K, *Nagai Y. Repeat-associated non-AUG translation in neuromuscular diseases: mechanisms and therapeutic insights. (review) J Biochem 173, 273–281 (2023). (J Biochem Special Issue)
  4. *Takeuchi T, Maeta K, Xin D, Oe Y, Takeda A, Inoue M, Nagano S, Fujihara T, Matsuda S, Ishigaki S, Sahashi K, Minakawa EN, Mochizuki H, Neya M, Sobue G, *Nagai Y. Sustained therapeutic benefits by transient reduction of TDP-43 using ENA-modified antisense oligonucleotides in ALS/FTD mice. Mol Ther Nucleic Acids 31, 353–366 (2023).
  5. Wang ET, Freudenreich CH, Gromak N, Jain A, Todd PK, *Nagai Y. What repeat expansion disorders can teach us about the Central Dogma. (review) Mol Cell 83, 324–329 (2023).
  6. Hatanaka Y., Umeda T., Shigemori K., Takeuchi T., Nagai Y., *Tomiyama T. C9orf72 hexanucleotide repeat expansion-related neuropathology is attenuated by nasal rifampicin in mice. Biomedicines 10, 1080 (2022)
  7. Fujino Y, *Nagai Y. The molecular pathogenesis of repeat expansion diseases. Biochem Soc Trans. 50(1):119-134 (2022) doi: 10.1042/BST20200143
  8. Ishiguro A, Lu J, Ozawa D, Nagai Y, Ishihama A. ALS-linked FUS mutations dysregulate G-quadruplex-dependent liquid-liquid phase separation and liquid-to-solid transition. J Biol Chem. 297(5):101284 (2021) doi: 10.1016/j.jbc.2021.101284
  9. Mori K, Gotoh S, Yamashita T, Uozumi R, Kawabe Y, Tagami S, Kamp F, Nuscher B, Edbauer D, Haass C, Nagai Y, Ikeda M. The porphyrin TMPyP4 inhibits elongation during the noncanonical translation of the FTLD/ALS-associated GGGGCC repeat in the C9orf72 gene. J Biol Chem. 297(4):101120 (2021) doi: 10.1016/j.jbc.2021.101120
  10. Oura S, Noda T, Morimura N, Hitoshi S, Nishimasu H, Nagai Y, Nureki O, Ikawa M. Precise CAG repeat contraction in a Huntington’s Disease mouse model is enabled by gene editing with SpCas9-NG. Commun Biol. 4(1):771 (2021) doi: 10.1038/s42003-021-02304-w
  11. Ishiguro T, *Nagai Y, Ishikawa K. Insight into spinocerebellar ataxia type 31 (SCA31) From Drosophila model. Front Neurosci. 15:648133 (2021) doi: 10.3389/fnins.2021.648133
  12. Shibata T, Nagano K, Ueyama M, Ninomiya K, Hirose T, Nagai Y, Ishikawa K, Kawai G, Nakatani K. Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat. Commun. 12(1), 236 (2021)
  13. Hervás R, Fernández-Ramírez M.D.C, Galera-Prat A, Suzuki M, Nagai Y, Bruix M, Menéndez M, Laurents D.V, Carrión-Vázquez M. Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. BMC Biol. 19(1), 43 (2021) doi: 10.1186/s12915-021-00967-9
  14. Minakawa E.N, Nagai Y. Protein aggregation inhibitors as disease-modifying therapies for polyglutamine diseases. Front【Review】 Neurosci. 15, 621996 (2021) doi: 10.3389/ fnins.2021.621996
  15. Minakawa E.N, Popiel H.A, Tada M, Takahashi T, Yamane H, Saitoh Y, Takahashi Y, Ozawa D, Takeda A, Takeuchi T, Okamoto Y, Yamamoto K, Suzuki M, Fujita H, Ito C, Yagihara H, Saito Y, Watase K, Adachi H, Katsuno M, Mochizuki H, Shiraki K, Sobue G, Toda T, Wada K, Onodera O, *Nagai Y. Arginine is a disease modifier of polyQ disease models that stabilizes polyQ protein conformation. Brain 143(6), 1811-1825 (2020)
  16. Araki K, Yagi N, Ikemoto Y, Hayakawa H, Fujimura H, Moriwaki T, Nagai Y, Murayama S, Mochizuki H. The secondary structural differences between Lewy body and glial cytoplasmic inclusion in autopsy brain with synchrotron FTIR micro-spectroscopy. Sci. Rep. 10(1), 19423 (2020) doi:10.1038/s41598-020-76565-6

森 康治（大阪大学大学院・医学系研究科・精神医学　助教）

  1. Fujino Y, Ueyama M, Ishiguro T, Ozawa D, Sugiki T, Ito H, Murata A, Ishiguro A, Gendron TF, Mori K, Tokuda E, Taminato T, Konno T, Koyama A, Kawabe Y, Takeuchi T, Furukawa Y, Fujiwara T, Ikeda M, Mizuno T, Mochizuki H, Mizusawa H, Wada K, Ishikawa K, Onodera O, Nakatani K, Taguchi H, Petrucelli L, *Nagai Y. FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD. eLife 12, RP84338 (2023).
  2. *Mori K, Shigenobu K, Beck G, Uozumi R, Satake Y, Suzuki M, Kondo S, Gotoh S, Yonenobu Y, Kawai M, Suzuki Y, Saito Y, Morii E, Hasegawa M, Mochizuki H, Murayama S, *Ikeda M. A heterozygous splicing variant IVS9-7A>T in intron 9 of the MAPT gene in a patient with right-temporal variant frontotemporal dementia with atypical 4 repeat tauopathy Acta Neuropathol Commun 11, 130 (2023)
  3. *Mori K, Gotoh S, Ikeda M. Aspects of degradation and translation of the expanded C9orf72 hexanucleotide repeat RNA. (review) J Neurochem, 166, 156-171 (2023).
  4. Taminato T, *Takeuchi T, Ueyama M, Mori K, Ikeda M, Mochizuki H, *Nagai Y. Therapeutic reduction of GGGGCC repeat RNA levels by hnRNPA3 suppresses neurodegeneration in Drosophila models of C9orf72-linked ALS/FTD. Hum Mol Genet 32, 1673–1682 (2023).
  5. Fujino Y, Mori K, *Nagai Y. Repeat-associated non-AUG translation in neuromuscular diseases: mechanisms and therapeutic insights. (review) J Biochem 173, 273–281 (2023). (J Biochem Special Issue)
  6. Czuppa M, Dhingra A, Zhou Q, Schludi C, König L, Scharf E, Farny D, Dalmia A, Täger J, Castillo-Lizardo M, Katona E, Mori K, Aumer T, Schelter F, Müller M, Carell T, Kalliokoski T, Messinger J, Rizzu P, Heutink P, *Edbauer D. Drug screen in iPSC-Neurons identifies nucleoside analogs as inhibitors of (G4C2)n expression in C9orf72 ALS/FTD. Cell Rep 39, 110913 (2022).
  7. *Mori K, Ikeda M. Biological basis and psychiatric symptoms in frontotemporal dementia. (review) Psychiatry Clin Neurosci 76, 351–360 (2022).
  8. Mori K*, Gotoh S, Yamashita T, Uozumi R, Kawabe Y, Tagami S, Kamp F, Nuscher B, Edbauer D, Haass C, Nagai Y, Ikeda M. The porphyrin TMPyP4 inhibits elongation during the noncanonical translation of the FTLD/ALS-associated GGGGCC repeat in the C9orf72 gene. J Biol Chem. Oct;297(4):101120 (2021) doi: 10.1016/j.jbc.2021.101120. Epub 2021 Aug 25. PMID: 34450161
  9. Kawabe Y, Mori K, Yamashita T, Gotoh S, Ikeda M. The RNA exosome complex degrades expanded hexanucleotide repeat RNA in C9orf72 FTLD/ALS. EMBO J. 39(19), e102700(2020) doi: 10.15252/embj.2019102700. Epub 2020 Aug 24.

松本有樹修（九州大学・生体防御医学研究所　准教授）

  1. Shiraishi C, *Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, *Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 14, 2131 (2023).
  2. Kito Y, *Matsumoto A, Ichihara K, Shiraishi C, Tang R, Hatano A, Matsumoto M, Han P, Iwasaki S, *Nakayama KI. The ASC-1 complex promotes translation initiation by scanning ribosomes. EMBO J 42, e112869 (2023).
  3. Ichihara K, *Nakayama KI, *Matsumoto A. Identification of unannotated coding sequences and their physiological functions. (review) J Biochem 173, 237–242 (2023). (J Biochem Special Issue)
  4. Higa T, Okita Y, Matsumoto A, Nakayama S, Oka T, Sugahara O, Koga D, Takeishi S, Nakatsumi H, Hosen N, Robine S, Taketo MM, Sato T, *Nakayama KI. Spatiotemporal reprogramming of differentiated cells underlies regeneration and neoplasia in the intestinal epithelium. Nat Commun 13, 1500 (2022).
  5. †Mise S, *†Matsumoto A, Shimada K, Hosaka T, Takahashi M, Ichihara K, Shimizu H, Shiraishi C, Saito D, Suyama M, Yasuda T, Ide T, Izumi Y, Bamba T, Kimura-Someya T, Shirouzu M, Miyata H, Ikawa M, *Nakayama KI. Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis. Nat. Commun. 28;13(1):1071 (2022)
  6. Nita A, *Matsumoto A, Tang R, Shiraishi C, Ichihara K, Saito D, Suyama M, Yasuda T, Tsuji G, Furue M, Katayama B, Ozawa T, Murata T, Dainichi T, Kabashima K, Hatano A, Matsumoto M, *Nakayama KI. A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing. PLoS Genet. 5;17(8):e1009686 (2021)
  7. Nita A, Muto Y, Katayama Y, Matsumoto A, Nishiyama M, Nakayama KI*. The autism-related protein CHD8 contributes to the stemness and differentiation of mouse hematopoietic stem cells. Cell Rep. 34(5), 108688 (2021)
  8. Kito Y, Matsumoto M, Hatano A, Takami T, Oshikawa K, Matsumoto A, Nakayama KI*. Cell cycle-dependent localization of the proteasome to chromatin. Sci. Rep. 10, 5801 (2020)

遠藤斗志也（京都産業大学・生命科学部　教授）・松本 俊介（九州大学・農学研究院　助教）

  1. Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Ganesan I, Wenz L-S, Becker T, Kikkawa M, Pfanner N, Wiedemann N, *Endo T. A multipoint guidance mechanism for β-barrel folding on the SAM complex. Nat Struct Mol Biol 30, 176–187 (2023).
  2. Matsumoto S, Ono S, Shinoda S, Kakuta C, Okada S, Ito T, Numata T, *Endo T. GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER. J Cell Biol 221, e202104076 (2022).
  3. Araiso Y, Imai K, *Endo T. Role of the TOM complex in protein import into mitochondria: structural views. Ann Rev Biochem 91, 679–703 (2022).
  4. Takeda H, Tsutsumi A, Nishizawa T, Lindau C, Busto JV, Wenz L-S, Ellenrieder L, Imai K, Straub SP, Mossmann W, Qiu J, Yamamori Y, Tomii K, Suzuki J, Murata T, Ogasawara S, Nureki O, Becker T, Pfanner N, Wiedemann N, Kikkawa M, *Endo T. Mitochondrial sorting and assembly machinery operates by β-barrel switching. Nature 590, 163–169 (2021).
  5. Araiso Y, Imai K, *Endo T. Structural snapshot of the mitochondrial protein import gate. FEBS J 288, 5300–5310 (2021).
  6. Shiino H, Furuta S, Kojima R, Kimura K, Endo T, Tamura Y. Phosphatidylserine fiux into mitochondria unveiled by organelle-targeted Escherichia coli phosphatidylserine synthase PssA. FEBS J. 288, 3285-3299 (2021) (Online published on Dec 7. 2020) doi: 10.1111/febs.15657
  7. Watanabe Y, Tamura Y, Kakuta C, Watanabe S, Endo T. Structural basis for inter-organelle phospholipid transport mediated by VAT-1. J Biol Chem. 295, 3257-3268 (2020)

松本 雅記（新潟大学大学院・医歯学総合研究科　教授）

  1. Funasaki S, Hatano A, Nakatsumi H, Koga D, Sugahara O, Yumimoto K, Baba M, *Matsumoto M, *Nakayama KI. A stepwise and digital pattern of RSK phosphorylation determines the outcome of thymic selection. iScience, 26(9):107552, 2023.
  2. Kito Y, *Matsumoto A, Ichihara K, Shiraishi C, Tang R, Hatano A, Matsumoto M, Han P, Iwasaki S, *Nakayama KI. The ASC-1 complex promotes translation initiation by scanning ribosomes. EMBO J 42, e112869 (2023).
  3. Shiraishi C, *Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, *Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 14, 2131 (2023).
  4. Aoyama S, *Nishida Y, Uzawa H, Himuro M, Kanai A, Ueki K, Ito M, Iida H, Tanida I, Miyatsuka T, Fujitani Y, Matsumoto M, Watada H. Monitoring autophagic flux in vivo revealed its physiological response and significance of heterogeneity in pancreatic beta cells. Cell Chem Biol 30, 658–671 (2023).
  5. Hatano A, Takami T, *Matsumoto M. In situ digestion of alcohol-fixed cells for quantitative proteomics. J Biochem 173, 243–254 (2023). (J Biochem Special Issue)
  6. Fujimoto M, Takii R, Matsumoto M, Okada M, Nakayama KI, Nakato R, Fujiki K, Shirahige K, *Nakai A. HSF1 phosphorylation establishes an active chromatin state via the TRRAP–TIP60 complex and promotes tumorigenesis. Nat Commun 13, 4355 (2022).
  7. Egami R, Kokaji T, Hatano A, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka K, Uematsu S, Terakawa A, Bai Y, Pan Y, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, *Kuroda S. Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle. iScience (2021)
  8. Johmura Y, Yamanaka T, Omori S, Wang T, Sugiura Y, Matsumoto M, Suzuki N, Kumamoto S, Yamaguchi K, Hatakeyama S, Takami T, Yamaguchi R, Shimizu E, Ikeda K, Okahashi N, Mikawa R, Suematsu M, Arita M, Sugimoto M, Nakayama KI, Furukawa Y, Imoto S, Nakanishi M. Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders. Science 371(6526): 265-70, (2021).
  9. Kokaji T, Hatano A, Ito Y, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka KI, Egami R, Terakawa A, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Ikeda K, Arita M, Matsumoto M, Nakayama KI, Hirayama A, Soga T, *Kuroda S. Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity. Sci. Signal. 13(660), eaaz1236 (2020)
  10. Tsukiyama T, Zou J, Kim J, Ogamino S, Shino Y, Masuda T, Merenda A, Matsumoto M, Fujioka Y, Hirose T, Terai S, Takahashi H, Ishitani T, Nakayama KI, Ohba Y, Koo BK. and Hatakeyama S. A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis. Nature Commun. 4586 (2020)
  11. Fang Y, Akimoto M, Mayanagi K, Hatano A, Matsumoto M, Matsuda S, Yasukawa T, Kang D. Chemical acetylation of mitochondrial transcription factor A occurs on specific lysine residues and affects its ability to change global DNA topology. Mitochondrion 53, 99-108 (2020)
  12. Nakagawa T, Hattori S, Nobuta R, Kimura R, Nakagawa M, Matsumoto M, Nagasawa Y, Funayama R, Miyakawa T, Inada T, Osumi N, Nakayama KI, Nakayama K. The AutismRelated Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression. iScience 23(4), (2020)
  13. Kito Y, *Matsumoto M, Hatano A, Takami T, Oshikawa K, Matsumoto A, *Nakayama KI. Cell cycle-dependent localization of the proteasome to chromatin. Sci. Rep. 10(1), 5801 (2020)
  14. Oshikawa K, *Matsumoto M, Kodama M, Shimizu H, *Nakayama KI. A failsafe system to prevent oncogenesis by senescence is targeted by SV40 small T antigen. Oncogene 39(10), 2170-86 (2020)

渡邉 力也（理化学研究所　主任研究員）

  1. Shinoda H, Taguchi Y, Nakagawa R, Makino A, Okazaki S, Nakano M, Muramoto Y, Takahashi C, Takahashi I, Ando J, Noda T, Nureki O, Nishimasu H, Watanabe R. Amplification-free RNA detection with CRISPR-Cas13. Commun Biol. 4(1), 476 (2021) doi: 10.1038/s42003-021-02001-8.
  2. Sakamoto S, *Komatsu T, *Watanabe R, Zhang Y, Inoue T, Kawaguchi M, Nakagawa H, Ueno T, Okusaka T, Honda K, *Noji H & *Urano Y. Multiplexed single-molecule enzyme activity analysis for counting disease-related proteins inbiological samples. Sci Adv. 6, eaay0888 (2020)

太田 元規（名古屋大学大学院・情報学研究科　教授）・福地佐斗志（前橋工科大学・工学部　教授）

  1. *Koike R, *Ota M, Elastic network model reveals distinct flexibilities of capping proteins bound to CARMIL and twinfilin-tail, Proteins, in press
  2. Anbo H, Sakuma K, Fukuchi S, *Ota M. How AlphaFold2 predicts conditionally folding regions annotated in an intrinsically disordered protein database, IDEAL. Biology 12, 182 (2023).
  3. Fukuchi S, Noguchi N, Anbo H, Homma K. Exon elongation added intrinsically disordered regions to the encoded proteins and facilitated the emergence of the last eukaryotic common ancestor. Mol Biol Evol 40, msac272 (2023).
  4. *Kanematsu Y, Narita A, Oda T, Koike R, Ota M, Takano Y, Moritsugu K, Fujiwara I, Tanaka K, Komatsu H, Nagae T, Watanabe N, Iwasa M, *Maéda Y, *Takeda S. Structures and mechanisms of actin ATP hydrolysis. Proc Natl Acad Sci USA 119, e2122641119 (2022).
  5. *Takeda S, Koike R, Fujiwara I, Narita A, Miyata M, Ota M, Maéda Y. Structural insights into the regulation of actin capping protein by twinfilin C-terminal tail, J Mol Biol 433, 166891 (2021)
  6. Takeda S, Koike R, Nagae T, Fujiwara I, Narita A, Maéda Y, Ota M. Crystal structure of human V-1 in the apo form. Acta Cryst. F 77, 13-21 (2021) doi:10.1107/ S2053230X20016829
  7. Koike R, Amano M, Kaibuchi K, Ota M. Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins. Prot. Sci. 29, 564-571 (2020) doi: 10.1002/pro.3789
  8. Anbo H, Amagai H and Fukuchi S. NeProc predicts binding segments in intrinsically disordered regions without learning binding region sequences. Biophys. Physicobiol. 17, 147-154 (2020)

 

公募研究

田中 良和（東北大学・生命科学研究科　教授）

  1. Watari H, Kageyama H, Masubuchi N, Nakajima H, Onodera K, Focia PJ, Oshiro T, Matsui T, Kodera Y, Ogawa T, Yokoyama T, Hirayama M, Hori K, Freymann DM, Komatsu N, *Araki M, *Tanaka Y, *Sakai R. A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation. Nat Commun 13, 7262 (2022).

松尾 芳隆（東京大学・医科学研究所　准教授）

  1. *Matsuo Y, Uchihashi T, *Inada T. Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex. Nat Commun 14, 79 (2023).
  2. Tomomatsu S, Watanabe A, Tesina P, Hashimoto S, Ikeuchi K, Li S, Matsuo Y, Beckmann R, *Inada T. Two modes of Cue2-mediated mRNA cleavage with distinct substrate recognition initiate No-go decay. Nucleic Acids Res. 51(1):253-270. (2023).
  3. Narita M, Denk T, Matsuo Y, Sugiyama T, Kikuguchi C, Ito S, Sato N, Suzuki T, Hashimoto S, Machova I, Tesina P, *Beckmann R, *Inada T. A distinct human disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation. Nat Commun 13, 6411 (2022).
  4. Li S, Ikeuchi K, Kato M, Buschauer R, Sugiyama T, Adachi S, Kusano H, Natsume T, Berninghausen O, Matsuo Y, Becker T, *Beckmann R, *Inada T. Sensing of individual stalled 80S ribosomes by Fap1 for non-functional rRNA turnover. Mol Cell 82, 3424–3437 (2022).

岩川 弘宙（東京大学・定量生命科学研究所　講師）

  1. *Iwakawa H, *Tomari Y. Life of RISC: Formation, action, and degradation of RNA-induced silencing complex. Mol Cell 82, 30–43 (2022).

今見 考志（京都大学大学院・薬学研究科　特任講師）

  1. Uchiyama J, Roy R, Wang DO, Morikawa K, Kawahara Y, Iwasaki M, Yoshino C, Mishima Y, *Ishihama Y, *Imami K. pSNAP: Proteome-wide analysis of elongating nascent polypeptide chains iScience 25, 104516 (2022).

花田 耕介（九州工業大学大学院・情報工学研究院　教授）

  1. Takeda T, Shirai K, Kim Y-W, Higuchi-Takeuchi M, Shimizu M, Kondo T, Ushijima T, Matsushita T, Shinozaki K, *Hanada K. A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana. Plant Mol Biol 111, 189-203 (2023)
  2. Oguchi R, Hanada K, Shimizu M, Mishio M, Ozaki H, Hikosaka K. Enhanced growth rate under elevated CO2 conditions was observed for transgenic lines of genes identified by intraspecific variation analyses in Arabidopsis thaliana Plant Molecular Biology 1-13 (2022)

町田 幸大（兵庫県立大学・工学研究科　准教授）

  1. Ito Y, *Chadani Y, Niwa T, Yamakawa A, Machida K, Imataka H, *Taguchi, H. Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes. Nat Commun 13, 7451 (2022).
  2. *Machida K, Miyawaki S, Kanazawa K, Hakushi T, Nakai T, Imataka H. An in vitro reconstitution system defines the defective step in the biogenesis of nutated β-actin proteins. ACS Synth Biol 10, 3158–3166 (2021).

藤岡 優子（微生物化学研究所　上級研究員）

  1. Ikeda R, Noshiro D, Morishita H, Takada S, Kageyama S, Fujioka Y, Funakoshi T, Komatsu-Hirota S, Arai R, Ryzhii E, Abe M, Koga T, Motohashi H, Nakao M, Sakimura K, Horii A, Waguri S, *Ichimura Y, *Noda NN, *Komatsu M. Phosphorylation of phase-separated p62 bodies by ULK1 activates a redox-independent stress response. EMBO J, in press (2023).

山形 敦史（理化学研究所　上級研究員）

  1. *Yamagata A, Murata Y, Namba K, Terada T, Fukai S, Shirouzu M. Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter. Nat Commun 13, 7180 (2022).

七野 悠一（理化学研究所・開拓研究本部　基礎科学特別研究員）

  1. †Miyake T, †Inoue Y, Shao X, Seta T, Aoki Y, Nguyen Pham KT, Shichino Y, Sasaki J, Sasaki T, Ikawa M, Yamaguchi Y, Okamura H, Iwasaki S, *Doi M. Minimal upstream open reading frame of Per2 mediates phase fitness of the circadian clock to day/night physiological body temperature rhythm Cell Rep, 112157 (2023).
  2. Chen M, Kumakura N, Saito H, Muller R, Nishimoto M, Mito M, Gan P, Ingolia NT, Shirasu K, Ito T, Shichino Y, *Iwasaki S. A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants eLife 12, e81302 (2023).
  3. †Miyake T, †Inoue Y, Shao X, Seta T, Aoki Y, Nguyen Pham KT, Shichino Y, Sasaki J, Sasaki T, Ikawa M, Yamaguchi Y, Okamura H, Iwasaki S, *Doi M. Minimal upstream open reading frame of Per2 mediates phase fitness of the circadian clock to day/night physiological body temperature rhythm Cell Rep 112157 (2023).
  4. *Shichino Y, *Iwasaki S. Compounds for selective translational inhibition Curr Opin Chem Biol 69, 102158 (2022).
  5. *Wu Q, Shichino Y, Abe T, Suetsugu T, Omori A, Kiyonari H, Iwasaki S, *Matsuzaki F. Selective translation of epigenetic modifiers affects the temporal pattern and differentiation of neural stem cells Nat Commun 13, 470 (2022).
  6. †Kashiwagi K, †Shichino Y, †Osaki T, Sakamoto A, Nishimoto M, Takahashi M, Mito M, Weber F, *Ikeuchi Y, *Iwasaki S, *Ito T. eIF2B-capturing viral protein NSs suppresses the integrated stress response Nat Commun 12, 7102 (2021).

足達 俊吾（産業技術総合研究所　主任研究員）

  1. Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, *Nishimasu H. RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Science 378, 882–889 (2022).