Biology subjects

Hagino, K.

Publications and source records attributed to Hagino, K..

5 recordsLinked to original sources

bioRxiv2026

Theoretical framework and experimental demonstration of sustainable in vitro regeneration of major translation factors EF-Tu and IF3

The development of molecular systems capable of self-regeneration, much like living organisms, is a major goal in synthetic biology. Previous efforts to expand the repertoire of regenerating proteins have relied on empirical optimization without a theoretical foundation, fundamentally limiting the scalability of this approach. Here, we developed the first theoretical framework, based on measurable parameters of translational proteins, to rationally predict the dilution rate that enables sustainable regeneration and the steady-state translation level. Using this framework, we successfully demonstrated sustainable regeneration of EF-Tu, the most abundant translation factor, for up to 15 rounds of serial dilution. We further extended this framework to the co-regeneration of multiple translation factors and demonstrated sustainable co-regeneration of EF-Tu and IF3, another major essential translation protein, for up to 20 rounds. These results establish a rational methodology for systematically expanding the number of regenerating proteins, providing a clear path toward the realization of a fully self-regenerating system.

Synthetic Biology↗

bioRxiv2026

Diel remodeling and cellular integration of the nitroplast

Nitrogen-fixing eukaryotes were not believed to exist in nature until the recent discovery of a N2-fixing organelle, or nitroplast, in the marine microalga Braarudosphaera bigelowii. This nitroplast (formerly known as UCYN-A2) has long been recognized as key cyanobacterial contributor to global oceanic N2 fixation. However, how this novel organelle is integrated and regulated within the architecture of a eukaryotic cell remains unclear. Here, we combine multiscale volumetric imaging with cryo-electron tomography to resolve the native architecture, cellular integration, and diel remodeling of the nitroplast in cultured and environmental cells. We find that the nitroplast occupies up to 10% of the cell volume and exhibits close interfaces with multiple host organelles through membrane contact sites, while integration of this metabolically demanding compartment does not disrupt global scaling of host organelles. Interestingly, the chloroplast-to-nitroplast volume ratio is conserved across distinct life stages. Cryo-electron tomography reveals that the nitroplast retains a reinforced four-layer cyanobacterial envelope and is additionally surrounded by two host-derived layers that remodel across the day-night cycle. During daytime N2 fixation, these host-derived barriers become locally discontinuous and the organelle interface becomes enriched with two distinct vesicle populations. Our findings suggest that dynamic control of organelle accessibility through transient membrane gating represents a fundamental strategy by which eukaryotic cells could domesticate new endosymbiotic functions during early organellogenesis.

cell biology↗

bioRxiv2026

Evolution of Translation Initiation Factor 2 Extensions Links Initiation to Bacterial Stress Response

Terminal extensions are recurrent features in protein evolution, often linked to environmental adaptation and novel regulatory or interaction functions. Here, we combine comparative genomics, structural modeling, and functional assays to elucidate the evolutionary diversification and functional significance of one of the key proteins of all cells, translation initiation factor 2 (IF2) terminal extensions across the tree of life. Specifically, we reconstruct the first comprehensive evolutionary map of IF2 across life, analyzing [~]800 homologs and classify seven distinct structural architectures of IF2 based on extension regions. These extensions are enriched for intrinsically disordered and phase-separation-promoting residues, suggesting roles beyond the conserved catalytic core. Further, functional characterization of IF2 with varying N-terminal lengths show that loss of the N-terminal extension slows bacterial growth specifically under temperature and pH stress. Appending C-terminal extensions from different organisms to the Escherichia coli IF2 demonstrates a conserved role for these extensions in adaptation to temperature and anaerobiosis. Our findings establish the functional significance of IF2 terminal extensions, linking their evolutionary diversification to stress-dependent regulation of translation.

microbiology↗

bioRxiv2025

Adapting a commercial anti-Aspergillus IgG ELISA kit for penguin sera: A novel approach using anti-chicken IgY antibody for the detection of anti-Aspergillus IgY titer

Penguins are susceptible to aspergillosis and are affected by the causative fungal pathogens Aspergillus spp., under immunocompromised conditions. Currently, there are limited serological tests available for diagnosing Aspergillus infections in penguins, highlighting the need for new diagnostic methods. While an anti-Aspergillus IgG detection kit using ELISA is commercially available and widely used in human medicine, it is not applicable for penguins because it incorporates anti-human antibodies as the secondary antibody for detection. To address this issue, an anti-chicken IgY antibody was incorporated into a commercial anti-Aspergillus IgG detection ELISA kit. First, anti-chicken IgY antibody was examined for cross-reactivity to penguin IgY, and the antibody recognized IgY from King, Gentoo, and African penguins in sera. Subsequently, serum samples from healthy penguins and penguins with aspergillosis were examined using anti-chicken IgY antibody incorporated into the anti-Aspergillus IgG ELISA kit. The results suggest that the combination method is applicable for the detection of anti-Aspergillus penguin IgY antibodies. However, because background titers can vary among individuals, we propose that routine monitoring could aid in the early detection of aspergillosis, even before the onset of symptoms.

microbiology↗

bioRxiv2024

Sustainable Regeneration of 20 Aminoacyl-tRNA Synthetases in a Reconstituted System Toward Self-Synthesizing Artificial Systems

In vitro construction of self-reproducible artificial systems is a major challenge in bottom-up synthetic biology. Here, we developed a reconstituted system capable of sustainably regenerating all 20 aminoacyl-tRNA synthetases (aaRSs), which are major components of the translation system. To achieve this, we needed five types of improvements: 1) optimization of aaRS sequences for efficient translation, 2) optimization of the composition of the translation system to enhance translation, 3) employment of another bacterial AlaRS and SerRS to improve each aminoacylation activity, 4) diminishing the translational inhibition caused by certain aaRS sequences by codon optimization and EF-P addition, and 5) balancing the DNA concentrations of 20 aaRSs to match each requirement. After these improvements, we succeeded in the sustainable regeneration of all 20 aaRSs for up to 20 cycles of 2.5-fold serial dilutions. These methodologies and results provide a substantial advancement toward the realization of self-reproducible artificial systems.

synthetic biology↗