Biology subjects

Hayama, K.

Publications and source records attributed to Hayama, K..

3 recordsLinked to original sources

bioRxiv2025

New Callicarpa (Lamiaceae) taxa: Two species and a natural hybrid from Hahajima Island, Ogasawara Islands, Japan

Two newly identified species of Callicarpa (Lamiaceae), C. boninensis and C. hahajimensis, along with a new natural hybrid, C. x chibusensis are described, all of which were identified on Hahajima Island, Ogasawara Islands, Japan. A comprehensive key to Callicarpa species in the Ogasawara Islands is also provided. Callicarpa boninensis, morphologically most similar to C. subpubescens, is distinguished by persistent stellate hairs on mature leaves and elongated petioles. Callicarpa hahajimensis, resembling C. parvifolia in the Chichijima Islands, differs in its reduced stellate hair density on both leaf surfaces and thinner leaves. Callicarpa x chibusensis, considered a natural hybrid between C. subpubescens and C. boninensis, is characterized by intermediate stellate hair densities--higher than in C. subpubescens but lower than in C. boninensis--on both leaf surfaces, smaller leaves than those of C. subpubescens, and a distinct flowering phenology relative to that of C. boninensis.

plant biology↗

bioRxiv2024

Structural insight into the nuclear transportation mechanism of PPARg by Transportin-1

The spatial and temporal control of protein is essential for normal cellular function. Proteins working in the nucleus have nuclear localization signal (NLS) sequences and are escorted into the nucleus by cognate nuclear transport receptors. A wealth of experimental data about NLS has been accumulated, and nuclear transportation mechanisms are established at the biochemical and structural levels. The peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors that control various biological responses. We recently reported that the transportation of PPAR{gamma} is mediated by Transportin-1, but PPAR{gamma} lacks a typical NLS sequence recognized by Transportin-1. Moreover, the recognition mechanism remains largely unknown. In this study, we determined the Cryo-EM structure of PPAR{gamma} in complex with Transportin-1 and revealed that Transportin-1 gripped the folded DNA binding domain and the Hinge region of PPAR{gamma}, indicating that PPAR{gamma} recognizes a folded domain with an extended region as a nuclear localization signal, not a canonical unstructured signal sequence, confirmed by the mutation analyses in vitro and in cultured cells. Our study is the first snapshot structure working in nuclear transportation, not in transcription, of PPAR{gamma}.

molecular biology↗

bioRxiv2022

Elucidating polymorphs of crystal structures with intensity-based hierarchical clustering analysis on multiple diffraction datasets

In macromolecular structure determination using X-ray diffraction from multiple crystals, the presence of different structures (structural polymorphs) necessitates the classification of diffraction data for appropriate structural analysis. Hierarchical clustering analysis (HCA) is a promising technique that has so far been used to extract isomorphous data, mainly for single structure determination. Although in principle the use of HCA can be extended to detect polymorphs, the absence of a reference for defining a threshold used for grouping the isomorphous datasets ( isomorphic threshold) poses a challenge. Here, we have applied unit cell-based and intensity-based HCAs to the datasets of apo-trypsin and inhibitor-bound trypsin that were mixed post-data acquisition to investigate how effective HCA is in classifying polymorphous datasets. Single-step intensity-based HCA successfully classified polymorphs with a certain isomorphic threshold. In datasets of several samples containing an unknown degree of structural heterogeneity, polymorphs could be identified by intensity-based HCA using the suggested isomorphic threshold. Polymorphs were also detected in single crystals using the data collected by the continuous helical scheme. These findings are expected to facilitate the determination of multiple structural snapshots by exploiting automated data collection and analysis. SynopsisSingle-step intensity-based hierarchical clustering is demonstrated to allow the detection of structural polymorphs in the diffraction datasets obtained from multiple crystals. By splitting the datasets collected by continuous helical scheme into several chunks, both inter and intra-crystal polymorphs can be successfully analyzed.

molecular biology↗