Biology subjects

Takasuka, T. E.

Publications and source records attributed to Takasuka, T. E..

3 recordsLinked to original sources

bioRxiv2026

Nitrogen metabolic map of Escherichia coli mediated by multi-functional aminotransferases

Nitrogen is a key element of organic molecules essential to all life. Unlike extensively characterized carbon metabolic maps, it remains elusive how assimilated nitrogen flows through metabolic networks. Here we determined the nitrogen metabolic map of Escherichia coli and used it to construct an enzyme-constrained metabolic model that includes multi-functionality of aminotransferase enzymes responsible for nitrogen transfer reactions. We characterized substrate specificities of sixteen E. coli aminotransferase enzymes by evaluating 2,528 reactions, uncovering 56 previously unrecognized activities. The cellular concentrations of these aminotransferase enzymes were quantified and used to estimate their catalytic rates across all enzyme-substrate pairs, leading to improved predictions of nitrogen flows in E. coli. This work advances our fundamental understanding of the nitrogen metabolic map critical for metabolism and growth.

biochemistry↗

bioRxiv2026

Structural determination of human nucleosomes reconstituted by the ExACT platform

The structure and function of eukaryotic chromatin have been extensively studied using conventional salt dialysis-based nucleosome assembly, which has provided fundamental structural insights into nucleosomes as well as a mechanistic understanding of their roles in DNA replication, repair and gene expression. Recently, we developed a labor-saving and time-efficient nucleosome assembly method using a wheat germ cell-free Expression and Assembly Coupled Technology (ExACT), which is emerging as a powerful tool for chromatin research. Here we report cryo-electron microscopy (cryo-EM) structures of human H3.1- and H3.3-containing nucleosomes assembled using this approach and validated by deep-learning-based amino acid-wise model quality (DAQ) scoring. The structures of H3.1- and H3.3-nucleosomes are nearly identical to previously reported models, confirming the structural fidelity of the method. In addition, we determined the previously unreported structure of the primate-specific H3.X-containing nucleosome. Together, these findings validate the cell-free co-expression nucleosome assembly platform and establish this method as a robust framework for biochemically investigating chromatin dynamics.

molecular biology↗

bioRxiv2026

A genomic and proteomic characterization of mannan-degradable Bacillus sp. TTS1, isolated from Tomakomai Forest in Hokkaido

A challenge in using plant biomass is its highly recalcitrant nature, which makes it economically infeasible to utilize. In natural environments, various microbes, including bacteria and fungi, are reported to decompose plant cell wall materials such as cellulose and hemicellulose, and there may be undescribed microbes that contribute to the degradation of plant biomass. We focused on isolating novel plant biomass-degrading bacteria and screened more than 100 isolates from the Tomakomai experimental forest in Hokkaido, Japan. Among them, one novel Bacillus species was chosen for whole-genome sequencing. Comparative genomics and a carbon source utilization assay indicated that the isolate belongs to a subspecies of Bacillus subtilis, which we named B. sp. TTS1. Glucose, cellobiose, xylose, xylan, mannose, or mannan was used as the sole carbon source in the minimum medium, and the growth of this bacterium was determined. Furthermore, a proteomic analysis of B. sp. TTS1 was performed using culture supernatants from various polysaccharide-containing media. In the present study, several key enzymes involved in plant biomass degradation were identified, namely {beta}-1,4-mannanase and xylanase, and they were highly enriched in all tested polysaccharides.

microbiology↗