Biology subjects

Satoh, H.

Publications and source records attributed to Satoh, H..

5 recordsLinked to original sources

bioRxiv2026

An enzyme-level benchmark based on environmental bacterial laccases for predicting contaminant fate in water

Bacterial laccases are widespread multicopper oxidases whose roles in the fate of anthropogenic chemicals in aquatic environments remain poorly understood. Here, we integrate metagenomic analysis, a miniaturized high-throughput assay and machine learning to establish an enzyme-level benchmark for predicting biotransformation of wastewater-relevant trace organic contaminants by laccase-mediator systems. Using a laccase from an ammonia-oxidizing bacterium as a model enzyme, we screened 183 compounds and identified 38 that underwent significant removal. Following phylogenetic analysis of environmental homologs, we expressed and purified two additional laccases from the bacterial methanotrophic phylum Methylmirabilota and an archaeal phylum Thermoproteota, demonstrating the activity of this enzyme family across domains. Graph convolutional network models trained on the dataset achieved up to 78% accuracy in classifying degradable versus persistent chemicals, while quantum-chemical descriptors highlighted key electronic properties governing oxidation. This bottom-up approach to enzyme-chemical interactions establishes a trajectory towards predicting contaminant persistence in engineered and natural waters.

biochemistry↗

bioRxiv2025

Humoral immunity induced by XEC monovalent vaccines against SARS-CoV-2 variants including XEC, LP.8.1, NB.1.8.1, XFG, and BA.3.2

After the emergence of SARS-CoV-2 Omicron variant at the end of 2021, Omicron has highly diverged into various sublineages: e.g., BA.5 in 2022, XBB.1.5 in 2023, JN.1 in 2024. Currently, several JN.1 subvariants including XEC, LP.8.1, NB.1.8.1 and XFG are circulating worldwide. Additionally, recent studies show that BA.3.2, a descendant of Omicron BA.3, exhibits profound immune evasion potential. On December 5, 2025, BA.3.2, was designated a variant under monitoring by the WHO. To prevent COVID-19, several countries including Japan have continuously developed and approved variant-adapted vaccines: e.g., ancestral/BA.5 bivalent vaccine in 20223, XBB.1.5-based monovalent vaccine in 20234, JN.1-based monovalent vaccine in 2024, and LP.8.1-based monovalent vaccine in 2025. Since XEC was more prevalent than LP.8.1 at the beginning of 2025 in Japan, two Japanese pharmaceutical companies, Daiichi Sankyo and Meiji Seika Pharma, have produced XEC-based vaccines. Here, we investigated the antiviral immunity induced by XEC-based monovalent vaccines against recently circulating SARS-CoV-2 variants, as well as BA.3.2, in the Japanese population. To assess the neutralizing antibody response induced by XEC-based vaccines, we obtained sera from individuals who had been vaccinated with the XEC-based mRNA monovalent vaccine produced by Daiichi Sankyo (N=22) or the XEC-based self-amplifying replicon vaccine produced by Meiji Seika Pharma (N=20). We collected sera before and 3-4 weeks after vaccination and then performed a neutralization assay using these sera with lentivirus-based pseudoviruses harboring spike proteins of B.1.1, BA.5, XBB.1.5, JN.1, XEC, LP.8.1, NB.1.8.1, XFG and BA.3.2. The 50% neutralization titers of the sera against all variants tested were significantly increased in after vaccination in both Daiichi Sankyo cohort (2.1-fold to 11.9-fold, P<0.0001) and Meiji Seika Pharma cohort (1.4-fold to 3.9-fold, P<0.0005). Consistent with our recent study using the sera from LP.8.1-based vaccinees, the humoral immunity induced by XEC-based vaccines against JN.1 and its subvariants (XEC, LP.8.1, NB.1.8.1 and XFG) was greater than that against other variants (B.1.1, BA.5, XBB.1.5 and BA.3.2). Notably, our result showed that the XEC-based mRNA vaccine induces a stronger humoral immunity compared to the XEC-based replicon vaccine, and even the LP.8.1-adapted vaccines. However, it should be noted that our cohorts are relatively small and may include confounding factors that affect the results, such as age, sex, history of natural infection and vaccination status. Future investigations with larger cohorts are required to better understand this possibility. To compare the immune status induced by XEC- and LP.8.1-based vaccines, we analyzed the cross-neutralization induced by these vaccines using antigenic cartography. The antigenic map was depicted based on the 50% neutralization titers values obtained from this study and our recent study using LP.8.1-based vaccine sera. The cartography showed that the immune status induced by XEC-based vaccines was similar to that induced by LP.8.1-based vaccines against the nine SARS-CoV-2 variant antigens tested. In sum, our investigations, including the recent one8, suggest that all 4 of the JN.1 subvariants-based vaccines that we tested induce profound humoral immunity against a broad range of SARS-CoV-2 variants.

microbiology↗

bioRxiv2025

Humoral immunity induced by LP.8.1 monovalent vaccines against a broad range of SARS-CoV-2 variants including XEC, NB.1.8.1, XFG, and BA.3.2

In the spring of 2025, multiple SARS-CoV-2 Omicron JN.1 subvariants were circulating, with LP.8.1 among the major variants. Pharmaceutical companies such as Pfizer/BioNTech, Moderna, and Novavax/Takeda adopted monovalent LP.8.1 for their 2025-2026 season vaccines, following recommendations issued by the WHO in May 2025. As of November 2025, SARS-CoV-2 variants including LP.8.1, XEC, NB.1.8.1, and XFG--all designated as variants under monitoring--were circulating. In terms of the spike gene, these recent variants as well as LP.8.1 are derived from JN.1. Moreover, BA.3.2, a BA.3 descendant with multiple mutations in the spike gene, has recently emerged and exhibits robust immune evasion. In Japan, the rollout of the LP.8.1-based vaccination has progressed since the end of September 2025. We previously reported the humoral immunity induced by the XBB.1.5-based monovalent vaccine in 2023 and the JN.1-based monovalent vaccine in 2024 in the Japanese population. Here, we investigated the efficiency of humoral immunity induced by two LP.8.1-based vaccines, the mRNA vaccine from Pfizer/BioNTech and the recombinant protein-based vaccine from Novavax/Takeda, in Japan. We performed neutralization assays using sera obtained from individuals who received the LP.8.1 mRNA vaccine from Pfizer/BioNTech (N=29) or the LP.8.1 recombinant protein vaccine from Novavax/Takeda (N=20) with pseudoviruses harboring spike proteins of B.1.1, BA.5, XBB.1.5, JN.1, LP.8.1, XEC, NB.1.8.1, XFG and BA.3.2. In both mRNA and protein-based vaccinee groups, the change in 50% neutralizing titer (NT50) against variants that were predominant before JN.1 (i.e., B.1.1, BA.5 and XBB.1.5) were smaller than those against JN.1 and its subvariants, including LP.8.1, XEC, NB.1.8.1 and XFG. Consistent with recent studies, neutralizing antibodies against BA.3.2 were induced by both vaccines. However, the induction fold change of BA.3.2 was smaller than those of JN.1 and its subvariants. Next, we tested humoral immune response of participants who received both JN.1-based vaccine in 2024 and LP.8.1-based vaccine in 2025 (N=15). Approximately a year after the JN.1-based vaccination, neutralization titer has waned against all variants tested. However, when we compare the NT50s of pre-vaccination sera between 2025 and 2024, those in 2025 against all variants except for B.1.1 were significantly higher than those last year. This suggests that the cross-neutralizing antibodies induced by JN.1-based vaccination were still maintained for a year. Furthermore, the neutralization abilities against the JN.1 sublineages tested and BA.3.2 were significantly reboosted after the LP.8.1-based vaccination. Our study shows immune boosting by the LP.8.1-based vaccine is effective in achieving cross-neutralization against a broad range of JN.1 sublineages in a JN.1-naive population and in recalling waning humoral immunity against these subvariants.

microbiology↗

bioRxiv2025

The protective role of chloroplast NADH dehydrogenase-like complex (NDH) against PSI photoinhibition under chilling stress

Chilling stress induces photosystem I (PSI) photoinhibition in various plants, severely impairing their growth. However, the mechanisms suppressing chilling-induced PSI photoinhibition remain unclear. This study aimed to identify factors preventing PSI photoinhibition by comparing two cucumber cultivars with different susceptibilities to PSI photoinhibition and chilling stress tolerance. In the chilling-sensitive cultivar, partial degradation of the CF1-{gamma} subunit of chloroplast ATPase led to uncoupling of the thylakoid membrane. In addition, electron efflux from Fe-S clusters downstream of PSI was restricted under chilling stress, resulting in highly reduced Fe-S clusters. Notably, this PSI over-reduction in the chilling-sensitive cultivar was observed not only under chilling stress but also under fluctuating light conditions, limited CO2 conditions, and during the transition from darkness to light, suggesting that cyclic electron flow contributes to cultivar differences in PSI photoinhibition. Indeed, the chilling-tolerant cultivar exhibited higher activity of the chloroplast NADH dehydrogenase-like complex (NDH) and suppressed reactive oxygen species (ROS) accumulation during the early stages of chilling stress. In contrast, in the chilling-sensitive cultivar, destabilization of PSI-NDH supercomplex under chilling stress led to the loss of NDH activity, resulting in severe PSI over-reduction. This study provides evidence that NDH acts as a crucial electron sink to prevent PSI photoinhibition and provides new insights into the mechanisms underlying low-temperature stress tolerance.

plant biology↗

bioRxiv2023

Microscopic and metatranscriptomic analyses revealed unique cross-domain symbiosis between Candidatus Patescibacteria/candidate phyla radiation (CPR) and methanogenic archaea in anaerobic ecosystems

To verify the parasitic lifestyle of Candidatus Patescibacteria in the enrichment cultures derived from a methanogenic bioreactor, we applied multifaceted approaches combining cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses. Cultivation experiments with the addition of exogenous methanogenic archaea with acetate, amino acids, and nucleoside monophosphates and 16S rRNA gene sequencing confirmed the increase in the relative abundance of Ca. Patescibacteria and methanogens. The predominant Ca. Patescibacteria were Ca. Yanofskybacteria and 32-520 lineages (to which belongs to class Ca. Paceibacteria) and positive linear relationships (r2 [≥] 0.70) between the relative abundance of Ca. Yanofskybacteria and Methanothrix, suggesting that the tendency of the growth rate is similar to that of the host. By fluorescence in situ hybridization (FISH) observations, the FISH signals of Methanothrix and Methanospirillum cells with Ca. Yanofskybacteria and with 32-520 lineages, respectively, were significantly lower than those of the methanogens without Ca. Patescibacteria, suggesting their parasitic interaction. The TEM and SEM observations also support parasitism in that the cell walls and plugs of these methanogens associated with submicron cells were often deformed. In particular, some Methanothrix-like filamentous cells were dented where the submicron cells were attached. Metatranscriptomic and protein structure prediction analyses identified highly expressed secreted genes from the genomes of Ca. Yanofskybacteria and 32-520, and these genes contain adhesion-related domains to the host cells. Considering the results through the combination of microscopic observations, gene expression, and computational protein modeling, we propose that the interactions between Ca. Yanofskybacteria and 32-520 belonging to class Ca. Paceibacteria and methanogenic archaea are parasitism.

microbiology↗