Biology subjects

Takami, H.

Publications and source records attributed to Takami, H..

4 recordsLinked to original sources

bioRxiv2026

Cooperative regulation of NF-E2 related factor 1 protein stability and transcriptional activation by endoplasmic reticulum-associated degradation system mediator, Selenoprotein S/K.

NRF1 is a key mediator of the proteasome recovery pathway, yet its regulation by ER-resident factors is not fully elucidated. Here, we demonstrate that selenoproteins SELS and SELK are critical regulators for NRF1 protein dynamics. SELS stabilizes NRF1, while SELK induces its insolubilization. Their deficiency leads to a hyper-accumulation and increased nuclear localization of NRF1 under proteasome inhibition condition. This results in an augmented transcriptional response of proteasome subunits. These results indicate that SELS and SELK cooperatively gate NRF1 activity by controlling its retrotranslocation and solubility, highlighting a novel layer of selenoprotein-mediated quality control in the proteostasis network.

biochemistry↗

bioRxiv2025

Identification and validation of liquid biopsy-based methylation biomarkers: a germ cell tumor subtype-specific study

Human germ cell tumors (GCTs) occur in infants, children, and adults, and present as germinomatous and/or non-germinomatous (embryonal carcinoma, teratoma, yolk sac tumor (YST), and choriocarcinoma) histologies at gonadal or extragonadal locations. Accurate subtyping is crucial for prognosis and treatment, but current clinical biomarkers lack sensitivity and specificity (serum proteins) or require a tissue biopsy (immunohistochemistry). Hence, less-invasive and improved subtype-specific biomarkers have potential for clinical utility. We conducted a meta-analysis of DNA methylation data (450K/EPIC array) from 15 (three original and 12 published) datasets including 713 GCTs, 109 healthy testis, and 221 healthy peripheral blood samples, revealing that GCT histology is the primary driver of methylation profiles, regardless of tumor location and patients age or sex. Per subtype, we identified differentially methylated regions as potential biomarkers. As proof of concept, we identified and validated two YST-specific biomarkers, i.e., APC and DPP7 promotor methylation, using methylation-sensitive restriction enzyme-based qPCR, of which DPP7 was also detectable in GCT serum-derived cell-free DNA. In conclusion, we present a novel method for in silico identification and in vitro and in vivo validation of YST subtype-specific liquid biopsy-based biomarkers. Our bioinformatic pipeline is easily transferrable encouraging additional applications in pan(pediatric)-cancer studies beyond GCTs.

cancer biology↗

bioRxiv2022

Distribution and survival strategies of diazotrophs in the Arctic Ocean revealed by global-scale metagenomic analysis

Nitrogen fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that nitrogen fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed genomes, including that of cyanobacterium UCYN-A (Candidatus Atelocyanobacterium thalassa), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Diazotrophs in the Arctic Ocean were either Arctic-specific or universal species. Arctic-specific diazotrophs, including Arctic UCYN-A, had unique gene sets (e.g., aromatics degradation) and/or a very small cell size (<0.2 {micro}m), suggesting adaptations to Arctic-specific conditions. Universal diazotrophs were generally heterotrophs and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters and polar regions. Thus both types of diazotroph have physiological traits adaptable to their environments, which allow nitrogen fixation on a global scale.

ecology↗

bioRxiv2018

The RopGEF KARAPPO is Essential for the Initiation of Vegetative Reproduction in Marchantia

Many plants can reproduce vegetatively, producing clonal progeny from vegetative cells; however, little is known about the molecular mechanisms underlying this process. Liverwort (Marchantia polymorpha), a basal land plant, propagates asexually via gemmae, which are clonal plantlets formed in gemma cups on the dorsal side of the vegetative thallus [1]. The initial stage of gemma development involves elongation and asymmetric divisions of a specific type of epidermal cell, called a gemma initial, which forms on the floor of the gemma cup [2, 3]. To investigate the regulatory mechanism underlying gemma development, we focused on two allelic mutants in which no gemma initial formed; these mutants were named karappo, meaning \"empty\". We used whole-genome sequencing of both mutants, and molecular genetic analyses to identify the causal gene, KARAPPO (KAR), which encodes a Rop guanine nucleotide exchange factor (RopGEF) carrying a PRONE catalytic domain. In vitro GEF assays showed that the full-length KAR protein and the PRONE domain have significant GEF activity toward MpRop, the only Rop GTPase in M. polymorpha. Moreover, genetic complementation experiments showed a significant role for the N- and C-terminal variable regions in gemma development. Our investigation demonstrated an essential role for KAR/RopGEF in the initiation of plantlet development from a differentiated cell, which may involve cell polarity formation and subsequent asymmetric cell division via activation of Rop signaling, implying a similar developmental mechanism in vegetative reproduction of various land plants.

plant biology↗