Biology subjects

Tajima, N.

Publications and source records attributed to Tajima, N..

4 recordsLinked to original sources

bioRxiv2025

Structural Basis of Inhibition and Desensitization in Heteromeric Kainate Receptors

Kainate receptors (KARs) mediate excitatory synaptic transmission and regulate neurotransmitter release. In the central nervous system, KARs predominantly exist as heterotetramers comprising low-affinity (GluK1-3) and high-affinity (GluK4-5) subunits, with GluK2/GluK5 being the most abundant. To elucidate their conformational transitions, we determined the cryo-electron microscopy (cryo-EM) structures of GluK2/GluK5 KARs in the apo and distinct ligand-bound states. The apo structure revealed compact packing with extensive inter-subunit interactions between the ligand-binding domains (LBDs) beyond the conserved D1-D1 upper-lobe contacts. The glutamate-bound structure exhibited enhanced packing that stabilized the desensitized conformation through increased intersubunit contacts relative to the homomeric KARs, indicating that the heterotetramers were conformationally less dynamic. To investigate subtype-specific antagonism, we engineered GluK2 and GluK5 mutants with altered affinities for the competitive antagonist UBP310. Structural analysis of these mutants revealed distinct UBP310 binding modes on the GluK2 versus the GluK5 subunits. Furthermore, we demonstrated that targeting GluK5 was more effective than targeting GluK2. Specifically, blocking GluK5 locked the receptor in a pore-occluded conformation, whereas antagonizing GluK2 retained structural flexibility above the pore. These findings provide a structural framework for understanding the distinct contributions of the GluK2 and GluK5 subunits to KAR function. TeaserCryo-EM structures of heteromeric kainate receptors reveal unique assembly and regulation mechanisms.

biophysics↗

bioRxiv2025

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of two wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

plant biology↗

bioRxiv2025

Structural Insights into Kainate Receptor Desensitization

Kainate receptors (KARs), along with AMPA and NMDA receptors, belong to the ionotropic glutamate receptor (iGluR) family and play critical roles in mediating excitatory neurotransmission throughout the central nervous system. KARs also regulate neurotransmitter release and modulate neuronal excitability and plasticity. Receptor desensitization plays a critical role in modulating the strength of synaptic transmission and synaptic plasticity. While KARs share overall structural similarity with AMPA receptors, the desensitized state of KARs differs strikingly from that of other iGluRs. Despite extensive studies on KARs, a fundamental question remains unsolved: why do KARs require large conformational changes upon desensitization, unlike other iGluRs? To address this, we present cryo-electron microscopy structures of GluK2 with double cysteine mutations in non-desensitized, shallow-desensitized and deep-desensitized conformations. In the shallow-desensitized conformation, two cysteine crosslinks stabilize the receptors in a conformation that resembles the desensitized state of AMPA receptors. However, unlike the tightly closed pore observed in the deep-desensitized KAR and desensitized AMPAR conformations, the channel pore in the shallow-desensitized state remains incompletely closed. Patch-clamp recordings and fluctuation analysis suggest that this state remains ion-permeable, indicating that the lateral rotational movement of KAR ligand-binding domains (LBDs) is critical for complete channel closure and stabilization of the receptor in desensitization states. Together with the multiple conformations representing different degree of desensitization, our results define the unique mechanism and conformational dynamics of KAR desensitization. HighlightsO_LIWe present cryo-EM structures of GluK2 kainate receptors with engineered cysteine crosslinks at the inter-dimer interface, which restrict subunit lateral rotation and attenuate receptor desensitization. C_LIO_LIThe structure of GluK2 double cysteine mutant in complex with the allosteric potentiator BPAM344 and glutamate represents a non-desensitized state, highlighting the critical conformational changes required for ion channel gating. C_LIO_LIThe glutamate-bound GluK2 mutant adopts multiple conformations, representing both shallow- and deep-desensitized states. Electrophysiological recordings indicate that the GluK2 kainate receptor mutant recovers from desensitization more rapidly, resembling AMPA receptors. Our structural and functional data suggest that shallow-desensitized KARs remain conductive, implying that the large lateral LBD rotation during KAR desensitization is essential for complete channel closure, distinguishing KARs from other iGluRs. C_LI

biophysics↗

bioRxiv2022

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)

Here, we report the first telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake), which consists of 13 chromosomes (spanning 160.7 Mb) and a 76 kb circular mitochondrial genome. The chromosome sequences were supported with telomeric repeats at the ends. GC-rich regions are located at the middle of the chromosomes and are enriched with long interspersed nuclear elements (LINEs). Repetitive sequences including long-terminal repeats (LTRs) and LINEs occupy 71.7% of the genome. A total of 28,322 potential protein-coding genes and 324 tRNA genes were predicted. Sequence and structure variant analysis revealed 2,322,349 single nucleotide polymorphisms and 102,831 insertions and deletions, 0.6% of which disrupted gene structure and function and were therefore classified as deleterious mutations. As many as 683 copies of the LTR retrotransposon MarY1 were detected in the matsutake genome, 91 of which were inserted in gene sequences. In addition, 187 sequence variations were found in the mitochondrial genome. The genomic data reported in this study would serve as a great reference for exploring the genetics and genomics of matsutake in the future, and the information gained would ultimately facilitate the conservation of this vulnerable genetic resource.

genomics↗