Biology subjects

Wakabayashi, Y.

Publications and source records attributed to Wakabayashi, Y..

11 recordsLinked to original sources

bioRxiv2026

OsPATROL1 overexpression accelerates stomatal opening to enhance photosynthetic induction and growth under fluctuating light in rice

Slow stomatal opening after increases in irradiance constrains carbon gain under fluctuating light, yet stomatal kinetics remain an underexplored target for crop improvement. Here, we investigated Oryza sativa PROTON ATPASE TRANSLOCATION CONTROL 1 (OsPATROL1), which encodes a Munc13-like protein implicated in stomatal regulation in Arabidopsis thaliana. OsPATROL1 overexpression had modest, condition-dependent effects on steady-state gas exchange and did not alter stomatal morphology or biochemical traits. In contrast, it consistently accelerated stomatal opening and photosynthetic induction, reducing the stomatal conductance time constant during induction by 41-43%. During 12 h of simulated natural fluctuating light, OsPATROL1-overexpressing plants maintained higher stomatal conductance and net CO2 assimilation rate, increasing cumulative assimilation by 8-12% while maintaining their intrinsic water-use efficiency (iWUE). Under artificial fluctuating light, overexpression alleviated growth reductions relative to steady light. Under glasshouse conditions, total biomass increased by 34-44%, accompanied by greater tiller number, root biomass, bleeding sap rate, and leaf nitrogen content. Taken together, these results indicate that OsPATROL1 overexpression accelerates stomatal opening, enhances photosynthetic induction and daytime carbon gain without compromising iWUE, and is associated with greater growth.

plant biology↗

bioRxiv2026

Rice brown spot resistance gene bsr1 also confers resistance to bacterial blight by suppressing sucrose efflux

Brown spot (BS), caused by the fungal pathogen Bipolaris oryzae, is a major disease threatening global rice production. However, the genetic basis of host BS resistance remains unclear. Here, we identified brown spot resistance 1 (bsr1), a quantitative trait locus conferring BS resistance, by map-based cloning. We show that bsr1 encodes a sucrose transporter and that a near-isogenic line carrying bsr1 (bsr1-NIL) in the susceptible Koshihikari genetic background exhibited resistance to BS by suppressing sucrose efflux into the apoplast after pathogen attack. Furthermore, bsr1-NIL also showed strain-specific resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae through the same mechanism. These findings demonstrate that bsr1 confers dual resistance to fungal and bacterial diseases by regulating sucrose efflux. Our study identifies a previously unrecognized mechanism underlying resistance to both BS and bacterial blight and highlights bsr1 as a promising target for breeding disease-resistance rice cultivars. Rice (Oryza sativa L.) is a staple food for more than half of the worlds population1. Brown spot (BS), caused by the fungus Bipolaris oryzae, is one of the most prevalent fungal diseases of rice, and its incidence has increased under global warming2. BS infects coleoptiles, leaves, leaf sheaths, panicle branches, glumes, and spikelets, and severe infection can substantially reduce grain yield.

plant biology↗

bioRxiv2026

Diversity and stability of the gut microbiome of naked mole-rat (Heterocephalus glaber), the longest-lived rodent

The naked mole-rat is a subterranean rodent adapted to extreme hypoxia and low metabolic demands, with an exceptionally long lifespan relative to its small body size, while maintaining reproductive capacity. Using 16S rRNA gene sequencing of 24 samples and whole-metagenome sequencing of 11 samples from individuals up to 15 years of age, we characterized the gut microbiota and showed its complexity and distinctiveness compared with that of other rodents, including mice, squirrels, and rabbits. Although all animals were born and raised in a laboratory setting, the gut microbiota remained taxonomically stable across ages and retained key taxa previously reported in wild naked mole-rats (e.g., Treponema and Desulfovibrio). Metagenome-assembled genomes revealed the presence of archaeal methanogens and termite-gut-associated bacteria (e.g., Methanobacteria within Euryarchaeota and Avelusimicrobium within Elusimicrobiota), together with genes involved in hydrogen metabolism and archaeal methanogenesis. Compared with mice, the naked mole-rat gut microbiota was enriched in carbohydrate-active enzymes targeting plant cell-wall polysaccharides, resembling those found in ruminants. We also detected evidence of flagellates, ciliates, and fungi, which may further contribute to polysaccharide degradation and fermentation, potentially within the enlarged cecum. Together, this comprehensive analysis provides distinctive gut microbial features of the naked mole-rat that may be associated with the naked mole-rats low metabolic rate and exceptional longevity.

microbiology↗

bioRxiv2026

Structural volume composition of internodes determines culm non-structural carbohydrates accumulation in rice

Non-structural carbohydrates (NSC) stored in the stem play a crucial role in supporting yield formation in rice. However, internode morphological determinants of NSC accumulation are unclear. This study aimed to clarify the relationship between internode morphology and NSC accumulation and to identify a robust morphological indicator for evaluating NSC accumulation capacity. Two years of field experiments were conducted using multiple cultivars. The NSC content was quantified for individual internodes and at the whole-plant culm level, and its relationships with internode morphological traits were analyzed. Since the upper internodes (UIN; first and second internodes) and lower internodes (LIN; third and subsequent internodes) exhibited contrasting roles in NSC accumulation, a novel index was introduced, the volume composition ratio (VCR) of UIN/LIN, which represents their relative volumetric contributions within a culm. The VCR of UIN/LIN showed the strongest correlation with culm NSC and high reproducibility across years, outperforming simple morphological traits. Manipulation of internode development using plant growth regulators demonstrated that altering VCR effectively modified culm NSC accumulation. Accordingly, the VCR of UIN/LIN serves as a robust morphological indicator of culm NSC accumulation capacity, providing a practical framework for improving NSC accumulation to achieve high and stable yield performance in rice. HighlightThis novel internode structural index robustly predicts the culm non-structural carbohydrate accumulation capacity, providing a practical morphological indicator for improving yield stability in rice.

plant biology↗

bioRxiv2025

Far-Red Light in Early Growth Stages Boosts Lettuce Biomass and Preserves Anthocyanins

Background and AimsLight plays a dual role in plants, serving as both an energy source and a regulator of development from seedling to senescence. Recently, far-red (FR) radiation has gained attention in the controlled environment agriculture (CEA) science and grower community for its potential to enhance yield through canopy expansion and improved light capture, contributing positively to photosynthesis. This study explores how supplemental FR light promotes lettuce growth and morphology across weekly intervals as well as analyzing photosynthetic parameters, pigment accumulation, and anthocyanin gene expression. MethodsRed leaf lettuce (Lactuca sativa Red Fire) was grown in a commercial plant factory with artificial light for six weeks. 5000K white (W) light was maintained at 300 mol m-2 s-1, and FR, when supplemented, was added at 100 mol m-2 s-1 in addition to the 300 mol m-2 s-1 of W light. Four lighting treatments were tested under a 16 h photoperiod: (1) W for all 6 weeks ("W"), (2) 4 weeks of W followed by 2 weeks of supplemental FR ("W to W+FR"), (3) 4 weeks of FR supplementation followed by 2 weeks of only W ("W+FR to W"), and (4) W+FR for all 6 weeks ("W+FR"). Key ResultsThe shoot dry weight after 6 weeks in "W+FR", "W+FR to W" and "W to W+FR" was greater than "W". Both "W+FR" and "W+FR to W" showed a tendency for greater canopy expansion compared to "W" as well as "W to W+FR". There were no significant differences in stomatal conductance among the treatments. On the other hand, in both "W" and "W+FR to W" plants, CO2 assimilation rates were enhanced when FR light was supplemented during measurement, compared to when FR was not provided. Anthocyanin accumulation was greater in both "W" and "W+FR to W", consistent with the expression of key genes involved in the anthocyanin biosynthesis pathway, including anthocyanin synthase (ANS), flavanone 3-hydroxylase (F3H) and dihydroflavonol 4-reductase (DFR). ConclusionsThis study demonstrates that FR supplementation during the early growth stages of lettuce promotes biomass accumulation by enhancing both canopy expansion and photosynthetic activity, while maintaining high levels of functional compounds such as anthocyanins.

physiology↗

bioRxiv2025

Pseudovirus-Mediated Proximity Labeling Identifies Candidate Host Cell Membrane Proteins Involved in Viral Attachment

Viral infections represent a significant threat to humanity, as exemplified by the COVID-19 pandemic. To mitigate the associated damage, it is essential to understand the biological characteristics of causative viruses. In this study, we report a novel method for identifying host cell molecules (including virus receptor) required for viral attachment, referred to here as "Host Cell Attachment Factors (HCAFs)". Our approach utilizes proximity labeling (PL) technology: pseudoviruses engineered to express a PL enzyme are applied to host cells, where they bind and initiate proximity labeling. Since HCAFs are expected to be localized near viral attachment sites, candidate HCAFs are specifically tagged by the PL process. Analysis of influenza HCAFs enabled the identification of multiple candidate molecules. Subsequent virus attachment experiments using CHO cells suggested that NRP1 may serve as an HCAF for influenza viruses. Given its simplicity and rapid turnaround, this method is adaptable to a wide range of enveloped viruses, including pandemic viruses that require emergency analysis.

microbiology↗

bioRxiv2025

Sustainable Edamame Production in an Artificial Light Plant Factory with Improved Yield and Quality

A plant factory utilizing artificial light is an innovative agricultural model that enables efficient and sustainable crop production. However, its application to a diverse range of crops remains limited. Edamame, a highly nutritious legume, has gained global popularity, yet its long-term storage is challenging due to quality deterioration, restricting its market distribution to seasonal availability. In this study, we successfully cultivated edamame using three hydroponic systems-- nutrient film technique (NFT), rockwool, and aeroponics (mist culture)--within an LED plant factory. Among these, NFT demonstrated the highest fresh seed yield, which was comparable to or exceeded that of conventional field cultivation. The high yield was attributed to enhanced pod formation and biomass production under controlled conditions. Furthermore, although free amino acid content was lower in NFT cultivation, NFT-grown edamame exhibited significantly higher total sugar and isoflavone contents than field-grown counterparts, suggesting superior eating quality and nutritional benefits. These results indicate that NFT hydroponics is a promising method for stable, high-yield edamame production with enhanced nutritional properties. This study provides a foundation for expanding edamame cultivation in controlled environments, contributing to year-round supply and its potential application in urban and space agriculture.

plant biology↗

bioRxiv2024

CENP-C-Mis12 complex establishes a regulatory loop through Aurora B for chromosome segregation

Establishing the correct kinetochore-microtubule attachment is crucial for faithful chromosome segregation. The kinetochore has various regulatory mechanisms for establishing correct bipolar attachment. However, how the regulations are coupled is not fully understood. Here, we demonstrate a regulatory loop between the kinetochore protein CENP-C and Aurora B kinase, which is critical for the error correction of kinetochore-microtubule attachment. This regulatory loop is mediated through the binding of CENP-C to the outer kinetochore Mis12 complex (Mis12C). Although the Mis12C binding region of CENP-C is dispensable for mouse development and proliferation in human RPE-1 cells, those cells lacking this region display increased mitotic defects. The CENP-C-Mis12C interaction facilitates the centromeric recruitment of Aurora B and the mitotic error correction in human cells. Given that Aurora B reinforces the CENP-C-Mis12C interaction, our findings reveal a positive regulatory loop between Aurora B recruitment and the CENP-C-Mis12C interaction, which ensures chromosome bi-orientation for accurate chromosome segregation.

cell biology↗

bioRxiv2024

Identification and Characterization of Compounds that Improve Plant Photosynthesis and Growth under Light Stress Conditions.

In order to satisfy the food and fuel demands of a growing population, global food production needs to increase by more than 50% before 2050. However, various environmental stresses in the natural environment inhibit plant growth and result in reduced yields. This is primarily caused by decreases in photosynthetic capacity. Thus, there is an urgent need to develop new strategies to improve agricultural productivity and ensure food security. In this study, a novel chemical-screening system with 96 well plates and leaf disks of tobacco was used to identify several anthraquinone derivatives that could relieve high light stress from plants. Treatments with these chemicals induced greater photosynthetic capacity after high light stress conditions for 20-72 hours (h) in tobacco and better plant growth after exposure to light stress for 96 hours in Arabidopsis and lettuces. The photoprotective effect of anthraquinone derivatives is closely related to chemical induced oxidation of PSI. Furthermore, there were no negative effects on plant growth in chemically treated plants under non-stressful conditions. Taken together, this study shows that anthraquinone derivatives can confer high light stress tolerance in plants, resulting in improved plant photosynthesis and growth in environments with light stress.

plant biology↗

bioRxiv2023

Global changes in open reading frame dominance of RNAs during cancer initiation and progression

Cancer cells express unique RNA transcripts; however, the factors determining their translation have remained unclear. We recently developed open reading frame (ORF) dominance as a measure that correlates with coding potential of RNAs. Upon calculating the ORF dominance of cancer-specific transcripts across 24 human tumor types, 14 exhibited significantly higher ORF dominance in cancer than in normal tissues. In organoid-based mouse genetic models, ORF dominance increased with carcinogenesis. Gene ontology analysis revealed that gene sets with increased ORF dominance were associated with cell proliferation, while those with decreased ORF dominance were linked to DNA damage response. Translatome analyses demonstrated that elevated ORF dominance during carcinogenesis resulted in higher translation frequencies of ribosome-bound RNAs. As cancer progressed, ORF dominance showed that the boundary between coding and noncoding transcripts became blurred prior to distant metastasis, indicating decreased proliferative cell populations and increased generation of RNA isoforms that potentially translate neoantigens before the development of metastatic tumors. These findings suggest that cancer evolution leads to dynamic changes in ORF dominance, resulting in global translational alterations in transcriptomes.

cancer biology↗

bioRxiv2022

Targeting c-Jun is a potential therapy of luminal breast cancer bone metastasis

Luminal breast cancer has the highest bone metastasis frequency among all breast cancer subtypes, but its metastatic mechanism has not been elucidated because of the lack of appropriate metastatic cell lines. The study aim was to characterize high-osteolytic bone metastatic MCF7-BM cell lines and extract c-Jun, a novel bone metastasis marker. We found that c-Jun was upregulated in MCF7-BM cells, and its deficiency was associated with suppression of the cell migration, transformation, and stemness of BM cells. In vivo, c-Jun-deficient MCF7-TAM67 cells exhibited weaker bone metastatic ability. Additionally, c-Jun overexpression in MCF7-BM cells led to a tumor-migration promotion cycle in the bone microenvironment possibly by enhancing calcium-induced migration and releasing the osteoclast activator BMP5. Inhibition of c-Jun by JNK-IN-8, a JNK inhibitor, effectively reduced tumorigenesis activities and bone metastatic tumors. Our results indicate the potential benefits of a therapy that targets c-Jun to prevent or minimize luminal breast cancer bone metastasis.

cancer biology↗