A5034100486- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Enzyme Structure and Function
- Bacterial Genetics and Biotechnology
- Selenium in Biological Systems
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- DNA and Nucleic Acid Chemistry
- Bacteriophages and microbial interactions
- Molecular Biology Techniques and Applications
- Microbial Natural Products and Biosynthesis
- Trace Elements in Health
- Mosquito-borne diseases and control
- Porphyrin Metabolism and Disorders
- Metalloenzymes and iron-sulfur proteins
- Photoreceptor and optogenetics research
- bioluminescence and chemiluminescence research
- Glutathione Transferases and Polymorphisms
- DNA Repair Mechanisms
- Diatoms and Algae Research
- Cancer-related gene regulation
- Viral Infections and Vectors
- Microbial Metabolic Engineering and Bioproduction
- Radiopharmaceutical Chemistry and Applications
RIKEN Center for Biosystems Dynamics Research
2018-2025
Saitama University
2025
RIKEN
1999-2024
Systems Biology Institute
2009-2018
The University of Tokyo
2008-2018
Synthetic Biologics (United States)
2014-2015
CLS Technology (Norway)
2014-2015
Tsurumi University
2011-2014
Tokyo University of Science
1995-2012
RIKEN Center for Integrative Medical Sciences
2004-2008
Transcription machinery remains steadfast Eukaryotic transcription of mRNA is a multistep process mediated by RNA polymerase II (Pol II). Pol combines with several other factors to form an elongation complex that promotes elongation. Ehara et al. determined the high-resolution structure means x-ray crystallography and cryo-electron microscopy (see Perspective Fouqueau Werner). Multiple are distributed on wide surface establish exit path DNA entry or tunnels, which facilitate nascent...
Genomic DNA forms chromatin, in which the nucleosome is repeating unit. The mechanism by RNA polymerase II (RNAPII) transcribes nucleosomal remains unclear. Here we report cryo-electron microscopy structures of RNAPII-nucleosome complexes RNAPII pauses at superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) nucleosome. major histone-DNA contact sites, interactions with subunits stabilize pause. These reveal snapshots transcription, gradually tears from histone surface while...
RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate the elongation Elf1 Spt4/5 cooperatively lower barriers increase RNAPII processivity nucleosome. cryo-electron microscopy structures of nucleosome-transcribing complexes (ECs) reveal reshape EC downstream edge intervene between They facilitate progression through...
During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo–electron microscopy, we obtained structures of RNAPII elongation complex (EC) passing through a nucleosome presence transcription factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C histone chaperone FACT (facilitates chromatin transcription). The show snapshots EC progression on DNA mediating downstream disassembly, followed by its reassembly upstream EC,...
Dengue is a mosquito-borne viral infection caused by dengue virus (DENV), member of the flaviviruses. The DENV genome 5'-capped positive-sense RNA with unique 5'-stem-loop structure (SLA), which essential for replication and 5' capping. virus-encoded proteins NS5 NS3 are responsible replication, but structural basis they cooperatively conduct required tasks has remained unclear. Here, we report cryoelectron microscopy (cryo-EM) structures SLA-bound (PC), NS3-bound PC (PC-NS3), an...
The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus , was solved and refined at 2.5 Å resolution. amino-terminal half GluRS shows geometrical similarity with that Escherichia coli glutaminyl-tRNA (GlnRS) the same subclass in I, comprising I-specific Rossmann fold domain intervening subclass-specific α/β domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then...
tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined crystal structure of SmpB in complex with entire tRNA domain from Thermus thermophilus. Overall, ribonucleoprotein (tRNP) mimics a long-variable-arm (class II tRNA) canonical L-shaped tertiary structure. The terminus corresponds to acceptor T arms, or upper part, tRNA. On other hand, simulates lower anticodon D stems, Intriguingly, several amino acid residues collaborate...
Dengue is a mosquito-borne viral infection that has spread globally in recent years. Around half of the world's population, especially tropics and subtropics, at risk infection. Every year, 50–100 million clinical cases are reported, more than 500,000 patients develop symptoms severe dengue infection: haemorrhagic fever shock syndrome, which threaten life Asia Latin America. No antiviral drug for available. The virus (DENV) non-structural protein 5 (NS5), possesses RNA-dependent RNA...
Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, mediated the adenosine triphosphate-dependent translocase/helicase Rho, which causes RNA/DNA dissociation from RNAP elongation complex (EC). However, structural basis of interplay between Rho remains obscure. Here, we report cryo-electron microscopy structure Thermus thermophilus EC engaged with Rho. The hexamer binds through carboxyl-terminal...
The Lys mutation of the canonical histone H3.1 Glu97 residue (H3E97K) is found in cancer cells. Previous biochemical analyses revealed that nucleosome containing H3E97K extremely unstable as compared to wild-type nucleosome. However, mechanism by which causes instability has not been clarified yet. In present study, cryo-electron microscopy structure entry/exit DNA regions are disordered, probably detachment nucleosomal from H3 N-terminal regions. This may change intra-molecular amino acid...
Translation elongation factor P (EF-P) stimulates ribosomal peptidyltransferase activity. EF-P is conserved in bacteria and essential for cell viability. Eukarya Archaea have an homologue, eukaryotic initiation 5A (eIF-5A). In the present study, we determined crystal structure of from Thermus thermophilus HB8 at a 1.65-Å resolution. consists three β-barrel domains (I, II, III), whereas eIF-5A has only two (N C domains). Domain I topologically same as N domain eIF-5A. On other hand, II III...
Overproducing Escherichia coli tRNA Glu in its homologous host results the presence of several distinctly modified forms this molecule that we name modivariants. The predominant modivariant wild‐type E. contains five nucleosides: Ψ13, mnm 5 s 2 U34, m A37, T54 and Ψ55. Four other overproduced modivariants differ from it by, respectively, either an additional Ψ, or lack A37 methylation combined with U34 U34. Chemical probing reveals anticodon loop is less reactive to probes than four others....
Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNASec) has an anticodon complementary to UGA codon. We solved crystal structure of human tRNASec. tRNASec a 9-bp acceptor stem and 4-bp T stem, contrast with 7-bp 5-bp canonical tRNAs. The kinked between U6:U67 G7:C66 base pairs, leading bent acceptor-T helix. 6-bp D 4-nt loop. long includes unique A14:U21 G15:C20a pairs. D-loop:T-loop interactions include pairs G18:U55 U16:U59, triple, U20:G19:C56. extra arm comprises...
DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2–engulfment and cell motility protein 1 (DOCK2•ELMO1) complex formation is required for DOCK2-mediated Rac signaling. In this study, we identified the N-terminal 177-residue fragment C-terminal 196-residue human DOCK2 ELMO1, respectively, as mutual binding regions, solved crystal structure...
The 21st amino acid, selenocysteine (Sec), is synthesized on its cognate transfer RNA (tRNA(Sec)). In bacteria, SelA synthesizes Sec from Ser-tRNA(Sec), whereas in archaea and eukaryotes SepSecS forms phosphoserine (Sep) acylated to tRNA(Sec). We determined the crystal structures of Aquifex aeolicus complexes, which revealed a ring-shaped homodecamer that binds 10 tRNA(Sec) molecules, each interacting with four subunits. N-terminal domain tRNA(Sec)-specific D-arm structure, thereby...
Significance In bacterial tRNAs with the 36 GG 37 sequence, where positions and are, respectively, third letter of anticodon 3′ adjacent to anticodon, modification N 1 -methylguanosine (m G) at position prevents +1 frameshifts on ribosome. The m G37 is introduced by enzyme TrmD, which harbors a deep trefoil knot within S -adenosyl-L-methionine (AdoMet)-binding site. We determined crystal structure TrmD homodimer in complex substrate tRNA an AdoMet analog. revealed how upon binding knot,...
We demonstrated X-ray structural analysis of the pressure-induced superconductor, $\beta'$-ET$_2$ICl$_2$ under extremely high-pressure conditions, where ET denotes bis(ethylenedithio)tetrathiafulvalene. This material has been known as highest transition temperature ($T_c$) superconductor among organic superconductors ($T_c=14.2$ K at $8.2$ GPa). On basis experimental results, ab-initio models were derived using constrained random phase approximation. revealed that Lifshitz exists behind Mott...