Biology subjects

Iwabuchi, K.

Publications and source records attributed to Iwabuchi, K..

7 recordsLinked to original sources

bioRxiv2026

USP10 Facilitates Homologous Recombination-Mediated DNA Double-Strand Break Repair through Localization to the Nucleolus

Ubiquitin-specific protease 10 (USP10) is a multifunctional deubiquitinating enzyme that primarily regulates cellular stress responses, including the DNA damage response. Here, we show that USP10 is required for homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs) and for the maintenance of genomic stability. USP10-depleted cells exhibit spontaneous micronuclei, impaired DSB repair following zeocin and camptothecin treatment, and reduced sister chromatid exchange. These cells are also more sensitive to irradiation and mitomycin C and display increased chromosomal abnormalities after mitomycin C treatment. Persistent RAD51 foci formation in USP10-depleted cells suggests that USP10 functions at a step downstream of RAD51 nucleofilament formation. This function of USP10 in facilitating HR repair depends on deubiquitinase activity but is independent of G3BP1/2 and PABP binding. In addition, a newly identified nucleolar localization signal is required for USP10s function in DSB repair. Together, these findings indicate that USP10 maintains genome integrity by localizing to the nucleolus and facilitating HR-mediated repair of DSBs.

cell biology↗

bioRxiv2024

Evolutionary acquisition of a primitive light-dependent nuclear relocation in Marchantia polymorpha

The terrestrialization of plants was accompanied by exposure to several environmental stresses. Adaptation to these stresses required numerous changes at the cellular and molecular level. One such adaptation in the leaves of Arabidopsis thaliana is the movement of cell nuclei to avoid UV damage. In the dark, the nuclei locate to the bottom walls of leaf cells to distance genetic material from external stresses, but in response to intense blue light (an indication of the presence of UV), they move to the side walls to escape UV-induced DNA damage1. The movement is driven by the photoreceptor phototropin and the actin cytoskeleton2. However, how this protective mechanism evolved in land plants remains unclear. Here, we show that in the liverwort Marchantia polymorpha, nuclei show a similar, but less stable movement in response to intense blue light. In the dark, M. polymorpha positioned nuclei on the upper walls of epidermal cells in young thalli, but in response to intense blue light, the nuclei immediately moved to the side walls, similar to A. thaliana. However, the movement was transient and the nuclei returned to the upper walls through both the actin and microtubule cytoskeletons. Unlike A. thaliana, M. polymorpha responded to prolonged (> 1 day) exposure to low light by moving nuclei from the upper to the side walls through both the actin and microtubule cytoskeletons and two photoreceptors (phototropin and phytochrome). However, no light-dependent nuclear relocation was observed in charophyte algae, suggesting that light-dependent nuclear relocation was initially established in the common ancestor of land plants as a result of terrestrialization and then diverged during land plant evolution.

plant biology↗

bioRxiv2024

Effect of phage variation on Shiga toxin 2 (Stx2) production and the virulence of Stx-producing Escherichia coli

Shiga toxin (Stx)-producing Escherichia coli (STEC) causes serious gastrointestinal illness, including hemorrhagic colitis and hemolytic uremic syndrome. Although all known Stxs (Stx1 and Stx2) are encoded by bacteriophages (Stx phages), the production of Stx2 is known to be a major risk factor for severe STEC infections. The production of Stx2, but not Stx1, is tightly coupled with the induction of Stx phages, and Stx2 production levels vary between STEC strains, even within the same serotype. Here, we analyzed the genomic diversity of all Stx phages in 71 strains representing the entire O145:H28 lineage, one of the major STECs. Our analysis revealed the highly dynamic nature of the Stx phages in O145:H28, including the independent acquisition of similar Stx phages by different sublineages and the frequent changes in Stx phages in the same sublineages due to the gain and loss of Stx phages. Analyses of Stx2 production levels in O145:H28 strains and K-12 lysogens of Stx2 phages of specific groups and types, which were defined by their early region sequences and CI repressors, respectively, revealed that short-tailed Stx2a phages (S-Stx2a phages) confer significantly greater Stx2 production to host strains than long-tailed Stx2a phages (L-Stx2a phages). However, L-Stx2a phages that encode a specific type of CI repressor promoted Stx2 production, comparable to the level of production among S-Stx2a phages, as well as promoted virulence to host strains, exceeding the level among other L-Stx2a phages. We also showed a clear link between the phage induction efficiency, which was primarily determined by the early region of each phage, and the level of Stx2 production by host strains. These results provide important insights into the diversification and dynamism of Stx phages and the relationship between the variations in Stx2 phages and the amount of Stx2 production by their host strains. Author summaryShiga toxin (Stx)-producing Escherichia coli (STEC) is an important human intestinal pathogen that causes severe illnesses. These bacteria produce Stx1, Stx2 or both toxins, but the production of Stx2 is an important measure of the virulence of STEC strains. While both types of Stx are encoded by bacteriophages (Stx phages), Stx2 production is tightly coupled with phage induction, and variations in Stx2 phages have been associated with variations in Stx2 production levels by their host O157:H7 STEC strains. However, in non-O157 STEC strains, the variation in Stx phages and its association with host strain production of Stx2 have not yet been fully analyzed. This systematic study of Stx phages in O145:H28 STEC reveals not only the marked genomic diversity and dynamism of Stx phages in this STEC lineage but also that short-tailed Stx2 phages and a specific group of long-tailed Stx2 phages induce high levels of Stx2 production by host strains, and this increased production is linked to the efficient induction of phages.

microbiology↗

bioRxiv2020

Unique habitat and macroinvertebrate assemblage structures in spring-fed streams: a comparison among lowland tributaries and mainstreams in northern Japan

The stable flow and temperature regimes of spring-fed streams are distinct from the dynamic regimes of other streams. We investigated differences in habitat and macroinvertebrate assemblages among three stream types (spring-fed tributary, non-spring-fed tributary and mainstream) in a clastic lowland of northern Japan. Current velocity was the slowest in the spring-fed reach, where the percent of fine sediment deposition was also 3.8-11.4 times higher than in the other stream types. The standing stock of detritus was also greater in the spring-fed reach. These results suggest that the stable flow regime in the spring-fed stream leads to the accumulation of fine sediment and detritus on the streambed. Oligochaeta and chironomids, which are burrower-gatherers, were remarkably abundant in the spring-fed reach. Total macroinvertebrate abundance was 3.8-12.2 times greater in the spring-fed reach than in the other stream types. Sprawler-grazer ephemeropterans were the most abundant in the mainstream reaches, likely due to higher primary productivity. Allomyia sp, which depend on cool spring-fed habitats, were found only in the spring-fed reach. The indicator species analysis also indicated multiple taxa of detritivores and Allomyia sp. for the spring-fed tributary. The macroinvertebrate assemblage in the spring-fed reach was characterized by numerous burrowers, collector-gatherers, and crenobiont taxa, highlighting the uniqueness and its contribution to enhance beta diversity in river networks.

ecology↗

bioRxiv2020

Genetic characterization of Streptococcus pyogenes emm 89 strains isolated in Japan from 2011 to 2019

Streptococcal toxic shock syndrome (STSS) caused by Streptococcus pyogenes emm89 strains has been increasing in several countries and reported to be linked with a recently emerged clade of emm89 strains, designated clade 3. In Japan, epidemiological and genetic information for emm89 strains remains elusive. In this study, we utilized emm89 strains isolated from both STSS (89 isolates) and non-STSS (72 isolates) infections in Japan from 2011 to 2019, and conducted whole-genome sequencing and comparative analysis, which resulted in classification of a large majority into clade 3 regardless of disease severity. In addition, STSS-associated genes and SNPs were found in clade 3 strains, including mutations of streptokinase (Ska), control of virulence sensor (CovS), serum opacity factor (SOF), sortase (SrtB), and fibronectin-binding protein F1 (PrtF1), and absence of the hylP1 gene encoding hyaluronidase. These findings provide insights into notable genetic features of emm89 strains.

microbiology↗

bioRxiv2019

A space-saving visual screening method, Glycine max FAST, for generating transgenic soybean

Soybean is an important crop plant for food and biofuel production, and there have been considerable efforts to develop transgenic soybean lines with higher seed oil contents and/or seed yields. However, the process of screening transgenic lines is laborious and requires a large amount of space. Here, we describe a powerful screening method, Glycine max Fluorescence-Accumulating Seed Technology (GmFAST), which is based on a seed-specific fluorescent marker. The marker is composed of a soybean seed-specific promoter coupled to the OLE1-GFP gene, which encodes GFP fused to the oil-body membrane protein OLEOSIN1 of Arabidopsis thaliana. We introduced the marker gene into cotyledonary nodes of G. max Kariyutaka via Agrobacterium-mediated transformation and regenerated heterozygous transgenic plants. OLE1-GFP-expressing soybean seeds can be selected nondestructively using a fluorescence stereomicroscope. Among T2 seeds, the most strongly fluorescent seeds were homozygous. GmFAST uses one-tenth of the growing space required for the conventional method. This space-saving method will contribute to facilitating transformation of soybean. OLE1-GFP was localized specifically to oil bodies in the cotyledon cells of seeds, but it did not affect oil content per seed, the size and density of the oil bodies, or oil composition. One of the homozygous lines (line #8) showed a 44% increase in the seed pod number, which resulted in 41% and 30% increases in seed yield and total oil production, respectively, compared with the wild type. In line #8, OLE1-GFP was inserted into the intron of Glyma13g30950, causing its overexpression. An increase in seed pod number was confirmed in Arabidopsis thaliana plants that overexpressed the Arabidopsis ortholog of Glyma13g30950, E6L1. These results suggest that line #8 is a valuable resource for agricultural and industrial applications. Taken together, GmFAST provides a space-saving visual and non-destructive screening method for soybean transformation, thereby increasing the chance of developing useful soybean lines.

plant biology↗

bioRxiv2019

A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop

The nucleus of mammalian cells is highly compartmentalized by nuclear bodies, including nuclear speckles. While nuclear bodies are known to function in regulating gene expression, their involvement in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, revealed that nuclear speckle factors regulating transcription are potentially involved in the regulation of HR. Among the top hits, we provide evidence showing that USP42, which is a deubiquitylating enzyme and a hitherto unidentified nuclear speckles factor, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localizes to nuclear speckles via an intrinsically disordered region, which is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. Mechanistically, USP42 antagonizes mono-ubiquitylation of DHX9 that is evoked after DSB induction. In conclusion, our data propose a model in which a novel nuclear speckle factor, USP42, facilitates DSB-induced R-loop resolution, BRCA1 loading to DSB sites and preferential DSB repair by HR, indicating the importance of spatial regulation of DSB repair choice mediated by nuclear bodies.\n\nSignificant statementDefects in the repair of DNA double-strand break (DSB), which is one of the most harmful DNA insults, cause human diseases including cancers. It has been suggested that DSBs generated in the coding region tend to be repaired by homologous recombination (HR) that is error-free DSB repair pathway. To reveal the spatial regulation of HR, in this study, we investigated the potential contribution of nuclear bodies, especially nuclear speckles, to HR, identifying a deubiquitylating enzyme USP42 as a HR promoting factor. We found that USP42 deubiquitylates DHX9, facilitates resolution of DNA-RNA hybrid structure and enhances HR through BRCA1 loading to DSB sites.\n\nClassificationBiological Sciences, Cell Biology

cell biology↗