Details of the Researcher

PHOTO

Seisuke Yamashita
Section
Advanced Research Center for Innovations in Next-Generation Medicine
Job title
Senior Assistant Professor
e-Rad No.
30769576

Research History 5

  • 2026/04 - Present
    Tohoku University　Advanced Research Center for Innovations in Next-Generation Medicine

  • 2019/11 - 2024/03
    東京大学大学院新領域創成科学研究科　メディカル情報生命専攻　助教

  • 2017/03 - 2019/10
    The University of Tokyo　Graduate School of Frontier Sciences

  • 2016/04 - 2017/02
    The University of Tokyo　Graduate School of Frontier Sciences

  • 2012/04 - 2016/03
    産業技術総合研究所　特別研究員

Education 2

  • 東京大学 大学院　理学系研究科　生物化学専攻

    2006/04 - 2012/03

  • The University of Tokyo　Faculty of Science　Department of Biophysics and Biochemistry

    2004/04 - 2006/03

Research Areas 1

  • Life sciences / Structural biochemistry /

Papers 21

  1. Mechanistic insights into Lin28-dependent oligo-uridylylation of pre-let-7 by TUT4

    Xiaojie Han, Seisuke Yamashita, Kozo Tomita

    Nucleic Acids Research　54　(1)　2026/01/05

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/nar/gkaf1421 　

    ISSN： 0305-1048

    eISSN： 1362-4962

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    Abstract Lin28-dependent oligo-uridylylation of precursor let-7 (pre-let-7) by terminal uridylyltransferases 4 and 7 (TUT4/7) represses let-7 expression by blocking Dicer processing, thereby regulating cell differentiation and proliferation. The interaction between the Lin28:pre-let-7 complex and the N-terminal Lin28-interacting module (LIM) of TUT4/7 is required for pre-let-7 oligo-uridylylation by the C-terminal catalytic module (CM). Here, we report the cryogenic electron microscopy structure of human TUT4 complexed with Lin28A and oligo-uridylated pre-let-7, representing the elongation stage of oligo-uridylylation. Structural and biochemical analyses suggest that, after recruitment of pre-let-7 to the LIM through interactions between its terminal stem-loop and Lin28A, the CM associates with the LIM through protein–protein interactions. The double-stranded stem region of pre-let-7 is surrounded by the CM and LIM, the upper portion of the duplex unwinds, and the 3′ end of pre-let-7 is positioned in the CM catalytic site for the initiation of oligo-uridylylation. At the oligo-uridylylation stage, the CM finger domain clamps the double-stranded region of pre-let-7, thereby further stabilizing the pre-let-7:TUT4 complex, enabling processive elongation of the uridine tail by the CM. Thus, the LIM functions as a stable anchor, working together with Lin28A to ensure efficient and processive oligo-uridylylation of pre-let-7.

  2. Cryo-EM structure of human TUT1:U6 snRNA complex Peer-reviewed

    Seisuke Yamashita, Kozo Tomita

    Nucleic Acids Research　53　(2)　2025/01/11

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/nar/gkae1314 　

    ISSN： 0305-1048

    eISSN： 1362-4962

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    Abstract U6 snRNA (small nuclear ribonucleic acid) is a ribozyme that catalyzes pre-messenger RNA (pre-mRNA) splicing and undergoes epitranscriptomic modifications. After transcription, the 3′-end of U6 snRNA is oligo-uridylylated by the multi-domain terminal uridylyltransferase (TUTase), TUT1. The 3′- oligo-uridylylated tail of U6 snRNA is crucial for U4/U6 di-snRNP (small nuclear ribonucleoprotein) formation and pre-mRNA splicing. Here, we present the cryo-electron microscopy structure of the human TUT1:U6 snRNA complex. The AUA-rich motif between the 5′-short stem-loop and the telestem of U6 snRNA is clamped by the N-terminal zinc finger (ZF)–RNA recognition motif and the catalytic Palm of TUT1, and the telestem is gripped by the N-terminal ZF and the Fingers, positioning the 3′-end of the telestem in the catalytic pocket. The internal stem-loop in the 3′-stem-loop of U6 snRNA is anchored by the C-terminal kinase-associated 1 domain, preventing U6 snRNA from dislodging on the TUT1 surface during oligo-uridylylation. TUT1 recognizes the sequence and structural features of U6 snRNA, and holds the entire U6 snRNA body using multiple domains to ensure oligo-uridylylation. This highlights the specificity of TUT1 as a U6 snRNA-targeting TUTase.

  3. Mechanism of U6 snRNA oligouridylation by human TUT1. International-journal

    Seisuke Yamashita, Kozo Tomita

    Nature communications　14　(1)　4686-4686　2023/08/10

    DOI： 10.1038/s41467-023-40420-9 　

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    U6 snRNA is a catalytic RNA responsible for pre-mRNA splicing reactions and undergoes various post-transcriptional modifications during its maturation process. The 3'-oligouridylation of U6 snRNA by the terminal uridylyltransferase, TUT1, provides the Lsm-binding site in U6 snRNA for U4/U6 di-snRNP formation and this ensures pre-mRNA splicing. Here, we present the crystal structure of human TUT1 (hTUT1) complexed with U6 snRNA, representing the post-uridylation of U6 snRNA by hTUT1. The N-terminal ZF-RRM and catalytic palm clamp the single-stranded AUA motif between the 5'-short stem and the 3'-telestem of U6 snRNA, and the ZF-RRM specifically recognizes the AUA motif. The ZF and the fingers hold the telestem, and the 3'-end of U6 snRNA is placed in the catalytic pocket of the palm for oligouridylation. The oligouridylation of U6 snRNA depends on the internal four-adenosine tract in the 5'-part of the telestem of U6 snRNA, and hTUT1 adds uridines until the internal adenosine tract can form base-pairs with the 3'-oligouridine tract. Together, the recognition of the specific structure and sequence of U6 snRNA by the multi-domain TUT1 protein and the intrinsic sequence and structure of U6 snRNA ensure the oligouridylation of U6 snRNA.

  4. Mechanism of tRNA recognition by heterotetrameric glycyl-tRNA synthetase from lactic acid bacteria. International-journal

    Yasuha Nagato, Seisuke Yamashita, Azusa Ohashi, Haruyuki Furukawa, Kazuyuki Takai, Kozo Tomita, Chie Tomikawa

    Journal of biochemistry　2023/06/01

    DOI： 10.1093/jb/mvad043 　

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    Glycyl-tRNA synthetases (GlyRSs) have different oligomeric structures depending on the organisms. While a dimeric α2 GlyRS species is present in archaea, eukaryotes, and some eubacteria, a heterotetrameric α2β2 GlyRS species is found in most eubacteria. Here, we present the crystal structure of heterotetrameric α2β2 GlyRS, consisting of the full-length α- and β-subunits, from Lactobacillus plantarum (LpGlyRS), gram-positive lactic bacteria. The α2β2  LpGlyRS adopts the same X-shaped structure as the recently reported E. coli α2β2 GlyRS. A tRNA docking model onto LpGlyRS suggests that the α- and β-subunits of LpGlyRS together recognize the L-shaped tRNA structure. The α- and β-subunits of LpGlyRS together interact with the 3'-end and the acceptor region of tRNAGly and the C-terminal domain of the β-subunit interacts with the anticodon region of tRNAGly. The biochemical analysis using tRNA variants showed that in addition to the previously defined determinants G1C72 and C2G71 base pairs, C35, C36 and U73 in eubacterial tRNAGly, the identification of bases at positions 4 and 69 in tRNAGly is required for efficient glycylation by LpGlyRS. In this case, the combination of a purine base at position 4 and a pyrimidine base at position 69 in tRNAGly is preferred.

  5. Structure of the Caenorhabditis elegans m6A methyltransferase METT10 that regulates SAM homeostasis. International-journal

    Jue Ju, Tomohiko Aoyama, Yuka Yashiro, Seisuke Yamashita, Hidehito Kuroyanagi, Kozo Tomita

    Nucleic acids research　2023/02/16

    DOI： 10.1093/nar/gkad081 　

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    In Caenorhabditis elegans, the N6-methyladenosine (m6A) modification by METT10, at the 3'-splice sites in S-adenosyl-l-methionine (SAM) synthetase (sams) precursor mRNA (pre-mRNA), inhibits sams pre-mRNA splicing, promotes alternative splicing coupled with nonsense-mediated decay of the pre-mRNAs, and thereby maintains the cellular SAM level. Here, we present structural and functional analyses of C. elegans METT10. The structure of the N-terminal methyltransferase domain of METT10 is homologous to that of human METTL16, which installs the m6A modification in the 3'-UTR hairpins of methionine adenosyltransferase (MAT2A) pre-mRNA and regulates the MAT2A pre-mRNA splicing/stability and SAM homeostasis. Our biochemical analysis suggested that C. elegans METT10 recognizes the specific structural features of RNA surrounding the 3'-splice sites of sams pre-mRNAs, and shares a similar substrate RNA recognition mechanism with human METTL16. C. elegans METT10 also possesses a previously unrecognized functional C-terminal RNA-binding domain, kinase associated 1 (KA-1), which corresponds to the vertebrate-conserved region (VCR) of human METTL16. As in human METTL16, the KA-1 domain of C. elegans METT10 facilitates the m6A modification of the 3'-splice sites of sams pre-mRNAs. These results suggest the well-conserved mechanisms for the m6A modification of substrate RNAs between Homo sapiens and C. elegans, despite their different regulation mechanisms for SAM homeostasis.

  6. Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance. International-journal

    Takayuki Ohira, Keiichi Minowa, Kei Sugiyama, Seisuke Yamashita, Yuriko Sakaguchi, Kenjyo Miyauchi, Ryo Noguchi, Akira Kaneko, Izumi Orita, Toshiaki Fukui, Kozo Tomita, Tsutomu Suzuki

    Nature　605　(7909)　372-379　2022/05

    DOI： 10.1038/s41586-022-04677-2 　

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    Post-transcriptional modifications have critical roles in tRNA stability and function1-4. In thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme growth temperatures5,6. Here we identified 2'-phosphouridine (Up) at position 47 of tRNAs from thermophilic archaea. Up47 confers thermal stability and nuclease resistance to tRNAs. Atomic structures of native archaeal tRNA showed a unique metastable core structure stabilized by Up47. The 2'-phosphate of Up47 protrudes from the tRNA core and prevents backbone rotation during thermal denaturation. In addition, we identified the arkI gene, which encodes an archaeal RNA kinase responsible for Up47 formation. Structural studies showed that ArkI has a non-canonical kinase motif surrounded by a positively charged patch for tRNA binding. A knockout strain of arkI grew slowly at high temperatures and exhibited a synthetic growth defect when a second tRNA-modifying enzyme was depleted. We also identified an archaeal homologue of KptA as an eraser that efficiently dephosphorylates Up47 in vitro and in vivo. Taken together, our findings show that Up47 is a reversible RNA modification mediated by ArkI and KptA that fine-tunes the structural rigidity of tRNAs under extreme environmental conditions.

  7. Mechanistic insights into m6A modification of U6 snRNA by human METTL16. International-journal Peer-reviewed

    Tomohiko Aoyama, Seisuke Yamashita, Kozo Tomita

    Nucleic acids research　2020/04/08

    DOI： 10.1093/nar/gkaa227 　

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    The N6-methyladenosine modification at position 43 (m6A43) of U6 snRNA is catalyzed by METTL16, and is important for the 5'-splice site recognition by U6 snRNA during pre-mRNA splicing. Human METTL16 consists of the N-terminal methyltransferase domain (MTD) and the C-terminal vertebrate conserved region (VCR). While the MTD has an intrinsic property to recognize a specific sequence in the distinct structural context of RNA, the VCR functions have remained uncharacterized. Here, we present structural and functional analyses of the human METTL16 VCR. The VCR increases the affinity of METTL16 toward U6 snRNA, and the conserved basic region in VCR is important for the METTL16-U6 snRNA interaction. The VCR structure is topologically homologous to the C-terminal RNA binding domain, KA1, in U6 snRNA-specific terminal uridylyl transferase 1 (TUT1). A chimera of the N-terminal MTD of METTL16 and the C-terminal KA1 of TUT1 methylated U6 snRNA more efficiently than the MTD, indicating the functional conservation of the VCR and KA1 for U6 snRNA biogenesis. The VCR interacts with the internal stem-loop (ISL) within U6 snRNA, and this interaction would induce the conformational rearrangement of the A43-containing region of U6 snRNA, thereby modifying the RNA structure to become suitable for productive catalysis by the MTD. Therefore, the MTD and VCR in METTL16 cooperatively facilitate the m6A43 U6 snRNA modification.

  8. Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme. International-journal Peer-reviewed

    Yining Liu, Anna Martinez, Seisuke Yamashita, Kozo Tomita

    Nucleic acids research　48　(3)　1572-1582　2020/02/20

    DOI： 10.1093/nar/gkz1216 　

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    BCDIN3 domain containing RNA methyltransferase, BCDIN3D, monomethylates the 5'-monophosphate of cytoplasmic tRNAHis with a G-1:A73 mispair at the top of an eight-nucleotide-long acceptor helix, using S-adenosyl-l-methionine (SAM) as a methyl group donor. In humans, BCDIN3D overexpression is associated with the tumorigenic phenotype and poor prognosis in breast cancer. Here, we present the crystal structure of human BCDIN3D complexed with S-adenosyl-l-homocysteine. BCDIN3D adopts a classical Rossmann-fold methyltransferase structure. A comparison of the structure with that of the closely related methylphosphate capping enzyme, MePCE, which monomethylates the 5'-γ-phosphate of 7SK RNA, revealed the important residues for monomethyl transfer from SAM onto the 5'-monophosphate of tRNAHis and for tRNAHis recognition by BCDIN3D. A structural model of tRNAHis docking onto BCDIN3D suggested the molecular mechanism underlying the different activities between BCDIN3D and MePCE. A loop in BCDIN3D is shorter, as compared to the corresponding region that forms an α-helix to recognize the 5'-end of RNA in MePCE, and the G-1:A73 mispair in tRNAHis allows the N-terminal α-helix of BCDIN3D to wedge the G-1:A73 mispair of tRNAHis. As a result, the 5'-monophosphate of G-1 of tRNAHis is deep in the catalytic pocket for 5'-phosphate methylation. Thus, BCDIN3D is a tRNAHis-specific 5'-monomethylphosphate capping enzyme that discriminates tRNAHis from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers.

  9. Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression. Peer-reviewed

    Yamashita S, Nagaike T, Tomita K

    Nature communications　10　(1)　1960　2019/04

    DOI： 10.1038/s41467-019-09966-5 　

  10. Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex. International-journal Peer-reviewed

    Yashiro Y, Yamashita S, Tomita K

    Structure (London, England : 1993)　27　(3)　476-484.e3　2019/03

    DOI： 10.1016/j.str.2018.11.005 　

    ISSN： 0969-2126

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    AtaT-AtaR is an enterohemorrhagic Escherichia coli toxin-antitoxin system that modulates cellular growth under stress conditions. AtaT and AtaR act as a toxin and its repressor, respectively. AtaT is a member of the GNAT family, and the dimeric AtaT acetylates the α-amino group of the aminoacyl moiety of methionyl initiator tRNAfMet, thereby inhibiting translation initiation. The crystallographic analysis of the AtaT-AtaR complex revealed that the AtaT-AtaR proteins form a heterohexameric [AtaT-(AtaR4)-AtaT] complex, where two V-shaped AtaR dimers bridge two AtaT molecules. The N-terminal region of AtaR is required for its dimerization, and the C-terminal region of AtaR interacts with AtaT. The two AtaT molecules are spatially separated in the AtaT-AtaR complex. AtaT alone forms a dimer in solution, which is enzymatically active. The present structure, in which AtaR prevents AtaT from forming an active dimer, reveals the molecular basis of the AtaT toxicity repression by the antitoxin AtaR.

  11. Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. International-journal Peer-reviewed

    Takaaki Taniguchi, Kenjyo Miyauchi, Yuriko Sakaguchi, Seisuke Yamashita, Akiko Soma, Kozo Tomita, Tsutomu Suzuki

    Nature chemical biology　14　(11)　1010-1020　2018/11

    DOI： 10.1038/s41589-018-0119-z 　

    ISSN： 1552-4450

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    Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N4-acetylcytidine (ac4C) is present at the anticodon first position (position 34) of bacterial elongator tRNAMet. Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac4C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac4C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac4C34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNAIle to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that ac4C34 modification of tRNAMet and L34 modification of tRNAIle act cooperatively to prevent misdecoding of the AUA codon.

  12. Crystal structures of U6 snRNA-specific terminal uridylyltransferase Peer-reviewed

    Seisuke Yamashita, Yuko Takagi, Takashi Nagaike, Kozo Tomita

    NATURE COMMUNICATIONS　8　15788　2017/06

    DOI： 10.1038/ncomms15788 　

    ISSN： 2041-1723

  13. Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA Peer-reviewed

    Anna Martinez, Seisuke Yamashita, Takashi Nagaike, Yuriko Sakaguchi, Tsutomu Suzuki, Kozo Tomita

    NUCLEIC ACIDS RESEARCH　45　(9)　5423-5436　2017/05

    DOI： 10.1093/nar/gkx051 　

    ISSN： 0305-1048

    eISSN： 1362-4962

  14. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL Peer-reviewed

    Taro Mannen, Seisuke Yamashita, Kozo Tomita, Naoki Goshima, Tetsuro Hirose

    JOURNAL OF CELL BIOLOGY　214　(1)　45-59　2016/07

    DOI： 10.1083/jcb.201601024 　

    ISSN： 0021-9525

    eISSN： 1540-8140

  15. Mechanism of 3 '-Matured tRNA Discrimination from 3 '-Immature tRNA by Class-II CCA-Adding Enzyme Peer-reviewed

    Seisuke Yamashita, Kozo Tomita

    STRUCTURE　24　(6)　918-925　2016/06

    DOI： 10.1016/j.str.2016.03.022 　

    ISSN： 0969-2126

    eISSN： 1878-4186

  16. Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme Peer-reviewed

    Seisuke Yamashita, Anna Martinez, Kozo Tomita

    STRUCTURE　23　(5)　830-842　2015/05

    DOI： 10.1016/j.str.2015.03.013 　

    ISSN： 0969-2126

    eISSN： 1878-4186

  17. Molecular insights into replication initiation by Q beta replicase using ribosomal protein S1 Peer-reviewed

    Daijiro Takeshita, Seisuke Yamashita, Kozo Tomita

    NUCLEIC ACIDS RESEARCH　42　(16)　10809-10822　2014/09

    DOI： 10.1093/nar/gku745 　

    ISSN： 0305-1048

    eISSN： 1362-4962

  18. Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase Peer-reviewed

    Seisuke Yamashita, Daijiro Takeshita, Kozo Tomita

    STRUCTURE　22　(2)　315-325　2014/02

    DOI： 10.1016/j.str.2013.12.002 　

    ISSN： 0969-2126

    eISSN： 1878-4186

  19. Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases Peer-reviewed

    Kozo Tomita, Seisuke Yamashita

    FRONTIERS IN GENETICS　5　36　2014/02

    DOI： 10.3389/fgene.2014.00036 　

    ISSN： 1664-8021

  20. Mechanism for Template-Independent Terminal Adenylation Activity of Q beta Replicase Peer-reviewed

    Daijiro Takeshita, Seisuke Yamashita, Kozo Tomita

    STRUCTURE　20　(10)　1661-1669　2012/10

    DOI： 10.1016/j.str.2012.07.004 　

    ISSN： 0969-2126

    eISSN： 1878-4186

  21. Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein Peer-reviewed

    Seisuke Yamashita, Takashi Nagata, Masahito Kawazoe, Chie Takemoto, Takanori Kigawa, Peter Guentert, Naohiro Kobayashi, Takaho Terada, Mikako Shirouzu, Motoaki Wakiyama, Yutaka Muto, Shigeyuki Yokoyama

    PROTEIN SCIENCE　20　(1)　118-130　2011/01

    DOI： 10.1002/pro.543 　

    ISSN： 0961-8368

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Research Projects 4

  1. DNA損傷部位における認識複合体形成の分子構造基盤

    山下 征輔

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 東北大学

    2026/04 - 2029/03

  2. ADPリボシル化酵素PARP7による自然免疫制御の分子構造基盤

    山下 征輔

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 東京大学

    2022/04/01 - 2025/03/31

  3. Structural basis for the RNA poly-uridylylation by human TUT1

    YAMASHITA Seisuke

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Early-Career Scientists

    Institution: The University of Tokyo

    2019/04/01 - 2022/03/31

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    TUT1 synthesizes the 3´-oligouridine tail required for the U6 snRNP formation and recycling. To reveal the detailed recognition mechanism of U6 snRNA by TUT1, we solved the X-ray crystal structure of human TUT1(hTUT1)-U6 snRNA complex. hTUT1 utilizes the multiple RNA-binding domains for recognition of the characteristic features of U6 snRNA. With these interactions, TUT1 specifically and efficiently interacts with U6 snRNA.

  4. Structural analysis of the poly A polymerase activated by oxidative stress

    Yamashita Seisuke

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Young Scientists (B)

    Institution: The University of Tokyo

    2016/04/01 - 2019/03/31

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    In this project, we aimed to reveal the molecular mechanisms of the specific nucleotidyl transfer by non-canonical nucleotidyl transferases. In particular, we focused on the structural and biochemical analyses of human Star-PAP and TUT4, which are the members of human non-canonical nucleotidyl transferases. We clarified the molecular basis for the U6 snRNA specific uridilylation by Star-PAP. We also clarified the molecular basis for the complex formation which is necessary for the inhibition of let-7 miRNA.