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顔写真

ヤマシタ　セイスケ

山下　征輔

Seisuke Yamashita

所属

高等研究機構未来型医療創成センター　研究部

職名

講師

学位

博士（理学）（東京大学）
修士（理学）（東京大学）

researchmap

https://researchmap.jp/yamashita-seisuke

J-GLOBAL ID

201801008643510129

e-Rad 研究者番号

30769576

経歴 5

2026年4月～継続中

東北大学　未来型医療創成センター　講師
2019年11月～ 2024年3月

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年3月～ 2019年10月

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　特任助教
2016年4月～ 2017年2月

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　特任研究員
2012年4月～ 2016年3月

産業技術総合研究所　特別研究員

学歴 2

東京大学大学院　理学系研究科　生物化学専攻

2006年4月～ 2012年3月
東京大学　理学部　生物化学科

2004年4月～ 2006年3月

研究分野 1

ライフサイエンス / 構造生物化学 /

論文 21

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年1月5日
出版者・発行元： 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.
Cryo-EM structure of human TUT1:U6 snRNA complex 査読有り

Seisuke Yamashita, Kozo Tomita

Nucleic Acids Research　53　(2)　2025年1月11日
出版者・発行元： 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.
Mechanism of U6 snRNA oligouridylation by human TUT1. 国際誌

Seisuke Yamashita, Kozo Tomita

Nature communications　14　(1)　4686-4686　2023年8月10日

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.
Mechanism of tRNA recognition by heterotetrameric glycyl-tRNA synthetase from lactic acid bacteria. 国際誌

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

Journal of biochemistry　2023年6月1日

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.
Structure of the Caenorhabditis elegans m6A methyltransferase METT10 that regulates SAM homeostasis. 国際誌

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

Nucleic acids research　2023年2月16日

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.
Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance. 国際誌

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年5月

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.
Mechanistic insights into m6A modification of U6 snRNA by human METTL16. 国際誌査読有り

Tomohiko Aoyama, Seisuke Yamashita, Kozo Tomita

Nucleic acids research　2020年4月8日

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.
Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme. 国際誌査読有り

Yining Liu, Anna Martinez, Seisuke Yamashita, Kozo Tomita

Nucleic acids research　48　(3)　1572-1582　2020年2月20日

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.
Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression. 査読有り

Yamashita S, Nagaike T, Tomita K

Nature communications　10　(1)　1960　2019年4月

DOI： 10.1038/s41467-019-09966-5 　
Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex. 国際誌査読有り

Yashiro Y, Yamashita S, Tomita K

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

DOI： 10.1016/j.str.2018.11.005 　

ISSN：0969-2126
Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. 国際誌査読有り

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

Nature chemical biology　14　(11)　1010-1020　2018年11月

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.
Crystal structures of U6 snRNA-specific terminal uridylyltransferase 査読有り

Seisuke Yamashita, Yuko Takagi, Takashi Nagaike, Kozo Tomita

NATURE COMMUNICATIONS　8　15788　2017年6月

DOI： 10.1038/ncomms15788 　

ISSN：2041-1723
Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA 査読有り

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

NUCLEIC ACIDS RESEARCH　45　(9)　5423-5436　2017年5月

DOI： 10.1093/nar/gkx051 　

ISSN：0305-1048

eISSN：1362-4962
The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL 査読有り

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

JOURNAL OF CELL BIOLOGY　214　(1)　45-59　2016年7月

DOI： 10.1083/jcb.201601024 　

ISSN：0021-9525

eISSN：1540-8140
Mechanism of 3 '-Matured tRNA Discrimination from 3 '-Immature tRNA by Class-II CCA-Adding Enzyme 査読有り

Seisuke Yamashita, Kozo Tomita

STRUCTURE　24　(6)　918-925　2016年6月

DOI： 10.1016/j.str.2016.03.022 　

ISSN：0969-2126

eISSN：1878-4186
Measurement of Acceptor-TΨC Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme. 査読有り

Yamashita S, Martinez A, Tomita K

Structure (London, England : 1993)　23　(5)　830-842　2015年5月

DOI： 10.1016/j.str.2015.03.013 　

ISSN：0969-2126

eISSN：1878-4186
Molecular insights into replication initiation by Qβ replicase using ribosomal protein S1. 査読有り

Takeshita D, Yamashita S, Tomita K

Nucleic acids research　42　(16)　10809-10822　2014年9月

DOI： 10.1093/nar/gku745 　

ISSN：0305-1048

eISSN：1362-4962
Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase 査読有り

Seisuke Yamashita, Daijiro Takeshita, Kozo Tomita

STRUCTURE　22　(2)　315-325　2014年2月

DOI： 10.1016/j.str.2013.12.002 　

ISSN：0969-2126

eISSN：1878-4186
Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases 査読有り

Kozo Tomita, Seisuke Yamashita

FRONTIERS IN GENETICS　5　36　2014年2月

DOI： 10.3389/fgene.2014.00036 　

ISSN：1664-8021
Mechanism for template-independent terminal adenylation activity of Qβ replicase. 査読有り

Takeshita D, Yamashita S, Tomita K

Structure (London, England : 1993)　20　(10)　1661-1669　2012年10月

DOI： 10.1016/j.str.2012.07.004 　

ISSN：0969-2126

eISSN：1878-4186
Structures of the first and second double-stranded RNA-binding domains of human TAR RNA-binding protein 査読有り

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年1月

DOI： 10.1002/pro.543 　

ISSN：0961-8368

︎全件表示 ︎最初の5件までを表示

共同研究・競争的資金等の研究課題 4

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

2026年4月～ 2029年3月
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

2022年4月1日～ 2025年3月31日
ヒトTUT1によるRNAポリウリジル化の分子構造基盤

山下征輔

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Early-Career Scientists

研究機関：The University of Tokyo

2019年4月1日～ 2022年3月31日

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TUT1はU6 snRNAの成熟化を担う酵素であり、U6 snRNAの3’末端にウリジンを付加する活性を持つ。U6 snRNAの3’末端はU6 snRNPの形成やスプライソソームのリサイクルに関わるため、その成熟化は真核生物の遺伝子発現に重要なプロセスである。本研究はTUT1によるU6 snRNA認識機構を原子レベルで明らかにすることを目的とし、ヒトTUT1とU6 snRNA複合体のX線結晶構造解析から立体構造を明らかにした。TUT1は複数のRNA結合ドメインでU6 snRNAの塩基配列や二次構造などの特徴を認識しており、全体として高い親和性と特異性で相互作用していることがわかった。
酸化ストレスにより活性化されるポリA付加酵素の構造機能解析

山下征輔

提供機関：Japan Society for the Promotion of Science

制度名：Grants-in-Aid for Scientific Research

研究種目：Grant-in-Aid for Young Scientists (B)

研究機関：The University of Tokyo

2016年4月1日～ 2019年3月31日

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本研究は、非古典的ヌクレオチド転移酵素による特異的な反応メカニズムの解明を目的として行われた。特にヒトのヌクレオチド転移酵素Star-PAPとTUT4をターゲットとしてX線結晶構造解析および生化学解析に取り組み、Star-PAPについてはU6 snRNAに対する特異的なウリジン付加反応の分子基盤を、TUT4についてはlet-7 miRNAの抑制に必要な複合体形成の分子基盤をそれぞれ明らかにした。