Biology subjects

Sugimoto, A.

Publications and source records attributed to Sugimoto, A..

15 recordsLinked to original sources

bioRxiv2026

Divergence of Cortical Force-Generating Mechanisms Underlies Differences in Spindle Behavior between C. elegans and C. inopinata

Microtubule-dependent pronuclear migration and mitotic spindle positioning are fundamental processes during the first embryonic division in many animals. In the one-cell embryo of Caenorhabditis elegans, these events are regulated by well-characterized pulling forces acting on astral microtubules, including cortical forces mediated by the G-GPR-LIN-5 dynein complex. Although the overall framework of these dynamics is conserved, recent studies have revealed substantial interspecies variation in their regulation. Here, we investigated nuclei and mitotic spindle behaviors in one-cell embryos of Caenorhabditis inopinata, the closest known relative of C. elegans, using live-cell imaging and functional perturbation. We found that C. inopinata embryos exhibit altered pronuclear migration, reduced anaphase spindle oscillations, and slower centrosome diffusion during telophase compared with C. elegans. These differences suggest weaker cortical pulling forces. Functional analyses using RNA interference showed that GPR retains its essential role in force generation, whereas the contribution of the microtubule depolymerizing kinesin KLP-7 is reduced in C. inopinata. Our results point to evolutionary changes in microtubule-regulated spindle dynamics, and provide insight into how conserved cellular processes can diversify through subtle changes in their underlying mechanisms.

cell biology↗

bioRxiv2026

Active and unusually expanded PIF/Harbinger transposable elements in the Caenorhabditis inopinata genome

BackgroundTransposable elements (TEs) serve as powerful drivers of genome innovation but also threaten genome integrity. The PIF/Harbinger superfamily is distinctive among DNA transposons because mobilisation typically requires proteins, a DDE transposase and a MADF DNA-binding protein. Caenorhabditis inopinata, the closest known relative of C. elegans, has a TE-rich genome and lacks multiple components of the ERGO-1-class endogenous small-RNA pathway, making it a useful system for examining TE dynamics in a distinct host context. We identified a spontaneous dumpy mutant of C. inopinata caused by insertion of a PIF/Harbinger-family element into the coding region of Cin-dpy-11. The inserted element, designated Harbinger-1M_cIno, belongs to the Turmoil2 lineage originally defined in C. elegans and retains a MADF domain but lacks a recognisable DDE transposase ORF. Genome-wide curation recovered 258 related copies, revealing a strongly asymmetric family structure. Short noncoding derivatives were predominant, MADF-bearing derivatives were expanded and only one DDE-bearing locus retained an apparently intact transposase gene, suggesting that DDE and MADF functions are partitioned across distinct elements and may be supplied in trans during mobilisation. We also identified a second PIF/Harbinger-derived family, Harbinger-2M_cIno, associated with the Turmoil1 lineage. This family comprises 1,376 copies and therefore records substantial past amplification, but it lacks a detectable DDE source, shows greater sequence divergence and more degraded terminal structures than Harbinger-1M_cIno. Together, these data indicate that the two PIF/Harbinger lineages in C. inopinata differ not in whether amplification occurred, but in when it occurred and whether present-day mobilisation competence has been retained.

genetics↗

bioRxiv2026

11β-HSD2 buffers fetal glucocorticoid exposure inducing Per1 expression under maternal stress

Glucocorticoids (GCs) have been proposed as maternal-fetal communication signals. However, fetal circadian rhythms are initially shielded from maternal entrainment, in addition to delayed circadian clock emergence due to CLOCK suppression. Premature CLOCK/BMAL1 activation disrupts Hes7-driven somite-like structure in gastruloids. Given the genomic proximity of Per1 to Hes7 and their transcriptional ripple effect, the physiological significance of delayed cell-autonomous circadian clock development and the temporal program of maternal-fetal communication during the developmental process have remained unclear. Here, based on a marked decline in Hsd11b2, encoding a GC-inactivating 11{beta}-HSD2 enzyme, during organogenesis, we performed split-litter embryo-transfer experiments in which Hsd11b2 knockout (KO) and wild-type (WT) embryos shared the same maternal environment. Amniotic fluid (AF) GCs remained low and arrhythmic under basal conditions. In contrast, maternal stress caused a pronounced GC surge and Per1 induction in KO, suggesting that 11{beta}-HSD2 buffers acute maternal GC surges. Despite the genomic proximity of Per1 to Hes7 and their transcriptional ripple effect, stress-associated and pharmacological GC exposure recapitulated no overt segmentation defects in vivo. Embryonic stem cell-derived gastruloid assays confirmed that neither GC exposure nor Per1 induction arrested Hes7 oscillations, whereas premature CLOCK/BMAL1 activation impaired these processes even in Hes7 KO gastruloid with ectopic rescue, suggesting that interference with the segmentation clock is mediated by premature CLOCK/BMAL1 activation, not by GC-induced Per1 expression. These findings clearly show that maternal GC signals are selectively buffered during early development. In addition, suppression of CLOCK/BMAL1 activity preserves segmentation clock function, indicating delayed circadian clock emergence is actively regulated during embryogenesis. Significance StatementGCs have been proposed as maternal-fetal communication signals. However, initially, circadian clock is not only suppressed but also shielded from maternal entrainment. Premature CLOCK/BMAL1 activation can disrupt Hes7-driven somitogenesis. In a split-litter Hsd11b2-knockout model, AF GCs remained low and arrhythmic basally but surged after maternal stress in KO embryos, inducing Per1. Despite a genomic position effect of Per1-Hes7 and their putative transcriptional coupling, stress-associated or pharmacological GC exposure did not cause segmentation defects in vivo or disrupt Hes7 oscillations in vitro, whereas CLOCK/BMAL1-driven arrest of Hes7 oscillations persisted in gastruloids despite ectopic Hes7 rescue. These findings identify 11{beta}-HSD2 as a developmental buffer and support the physiological importance of the temporal architecture controlling the timing of circadian clock development.

developmental biology↗

bioRxiv2026

A Fluorescent Dauer Marker in Caenorhabditis inopinata Enables Comparative Analysis of Dauer-Inducing Mechanisms

Dauer larvae are a dormant developmental stage in nematodes that is induced by a range of environmental cues. The molecular mechanisms that transduce these cues to regulate dauer entry have been well characterized in Caenorhabditis elegans, whereas those in other nematode species remain unclear. The closest known sibling species of C. elegans, Caenorhabditis inopinata, occupies a distinct ecological niche and shows an extremely low frequency of dauer formation by starvation in laboratory conditions, suggesting that it could serve as a useful comparative model for analyzing dauer-inducing mechanisms. To support such analysis, we generated a fluorescent dauer reporter, Cin-col-183p::mCherry, in C. inopinata based on a previously reported dauer-specific reporter in C. elegans. This reporter showed fluorescence specifically in the pre-dauer and dauer stages, but not in other developmental stages, indicating that it functions as a dauer-specific marker in C. inopinata. Using these marker strains, we compared the responses to high temperature and RNAi-mediated knockdown of insulin/IGF-1 pathway genes (daf-2, age-1, and pdk-1), and found that dauer induction differs mechanistically between C. elegans and C. inopinata. This dauer-specific fluorescent strain will be a useful tool for investigating the diversity of dauer-inducing mechanisms across nematode species. Article SummaryDauer is a dormant developmental stage in nematodes induced by environmental stress. Although its regulation is well studied in Caenorhabditis elegans, the mechanisms in other species remain unclear. Here, we developed a fluorescent dauer reporter, Cin-col-183p::mCherry, in Caenorhabditis inopinata, a close relative of C. elegans. The reporter was specifically expressed in pre-dauer and dauer stages, confirming its usefulness as a dauer marker. Using this strain, we found that responses to high temperature and insulin/IGF-1 pathway gene knockdown differ between C. elegans and C. inopinata. This reporter will help reveal diversity in dauer-inducing mechanisms across nematode species.

developmental biology↗

bioRxiv2025

Programmed DNA elimination was present in the last common ancestor of Caenorhabditis nematodes

In most organisms, all cells inherit the same genome, and many mechanisms exist to preserve its integrity across cell divisions. Programmed DNA elimination (PDE), the targeted removal of specific genomic regions from somatic cell lineages during early embryogenesis, is a striking exception. Since its discovery in parasitic nematodes over a century ago, PDE has been observed in diverse eukaryotes, including ciliates, arthropods, and vertebrates. However, the mechanisms, functions, and evolutionary origins of PDE remain poorly understood. Here, we describe the discovery of PDE in three species of the free-living nematode genus Caenorhabditis. Multiple genomic regions are precisely eliminated from somatic cells during early embryogenesis, resulting in chromosome fragmentation and the loss of key germline genes. The sites of elimination are strongly associated with conserved sequence motifs that likely direct DNA breakage. Comparative analyses indicate that PDE was present in the last common ancestor of Caenorhabditis and subsequently lost early during the evolution of many species, including C. elegans. The presence of PDE in the ancestors of one of biologys most important model organisms, together with recent discoveries in other eukaryotic lineages, reveals PDE to be a far more widespread and significant feature of evolution and development than previously recognised.

evolutionary biology↗

bioRxiv2025

Generation of antigen-specific and functionally stable Treg cells from effector/memory T cells for cell therapy of immunological diseases

One strategy for antigen-specific immunosuppression is to convert antigen-specific conventional T cells (Tconvs) into Foxp3+ regulatory T cells (Tregs) that are as stably suppressive as naturally occurring Tregs (nTregs). To achieve the conversion in vitro for mice and humans, we induced high Foxp3 expression in antigen- and IL-2-stimulated Tconvs by CDK8/19 inhibition, and established Treg-specific epigenetic changes by depriving CD28 co-stimulation during in vitro Treg induction to specifically promote the expression of Treg signature genes, especially Foxp3. Repeating this process, with intermittent resting cultures containing IL-2 only, enabled in a short duration efficient conversion of naive as well as effector/memory CD4+ Tconvs, including Th1, Th2 and Th17 cells, into Foxp3+ Tregs, which were similar to nTregs in transcription and epigenetic modification. Induced Tregs (iTregs) thus generated were indeed functionally and phenotypically stable in vivo and effectively suppressed inflammatory bowel disease and graft-versus-host disease in mouse models. Adoptive cell therapy with such effector/memory Tconv-derived, functionally stable, iTregs would be able to achieve antigen- and disease-specific treatment of immunological diseases. One Sentence SummaryAntigen-specific and functionally stable Treg cells can be generated in vitro from effector/memory T cells for cell therapy of immunological diseases.

immunology↗

bioRxiv2025

Oral antigen exposure under co-stimulation blockade generates Treg cells to establish immune tolerance despite prior sensitization

Antigen-specific oral tolerance is effective in preventing harmful immune responses in antigen-non-sensitized animals but difficult to be induced in those already antigen-primed. Here, we show in mice that feeding of antigen-containing diet generates peripherally derived regulatory T (pTreg) cells that exhibit a tissue-adapted effector phenotype. The antigen feeding also enables the generated pTreg cells to acquire Treg-specific epigenomic changes in Treg signature genes including Foxp3, hence the stability of Treg-specific function. Cessation of antigen feeding, however, results in decline in oral tolerance with diminution of pTreg cells. Transcriptomic analysis has revealed that the induced pTreg cells predominantly express CD101. CD101+ Treg cells with a similar phenotype and epigenetic alterations can also be generated in vitro from antigen-primed naive CD4+ T cells by blockade of CD28-mediated co-stimulation during TGF-{beta}-dependent Treg induction. Furthermore, in vivo CD28 signal blockade by CTLA-4-immunoglobulin fusion protein (CTLA4-Ig) before antigen feeding can establish oral tolerance in the mice precedingly antigen-sensitized by a non-oral route. The blockade facilitates differentiation of antigen-specific conventional T cells into CD101+ pTreg cells. Thus, continuous oral antigen administration combined with CD28 co-stimulation blockade generates CD101+ antigen-specific functionally stable pTreg cells, which can establish long-term systemic antigen-specific immune tolerance even in antigen-pre-sensitized animals.

immunology↗

bioRxiv2024

Dramatic evolutionary changes of conserved noncoding elements accompanied by extraordinary features of Caenorhabditis inopinata

Phenotypic evolution is driven by genetic mutations occurring in both protein-coding and noncoding regions of the genome. Conserved noncoding elements (CNEs) have--at least partially--gene regulatory functions and contribute to the evolution of organisms by altering their gene expression. Evolutionary changes in CNEs, including their loss and accelerated evolution, can play crucial roles in shaping species-specific traits. The extensive functional genomic information available for the model nematode Caenorhabditis elegans, together with the recent accumulation of high-quality genome sequences from related species, has made Caenorhabditis nematodes a powerful system for comparative genomics focused on CNE evolution. The recently described species Caenorhabditis inopinata has several peculiar traits notable for its unusually large body size and is regarded as an appropriate species that links phenotypic evolution with genomic changes. Here, using comparative genomics and transcriptomics in C. inopinata, we analyzed the evolution of CNEs and inferred their influence during phenotypic evolution. We detected substantial evolutionary changes in CNEs in C. inopinata compared to other relatives--changes frequently associated with body morphology and behavior corresponding to distinct ecological traits. Our findings suggest that loss and accelerated evolution of CNE are associated with species-specific traits and provide new insight into the impact of noncoding elements on evolution. Significance statementLarge-scale phenotypic evolution has been observed across a wide range of taxa and may be accompanied by substantial genomic changes. Caenorhabditis inopinata, a nematode species closely related to C. elegans, shows several distinctive morphological and behavioral traits compared with its congeners, and through comparative genomics and transcriptomics, we identify substantial evolutionary changes in conserved noncoding elements (CNEs)-- including their loss and accelerated sequence evolution. Furthermore, these changes are frequently associated with genes involved in morphology and behavior, suggesting a potential link between CNE evolution and species-specific phenotypes.

evolutionary biology↗

bioRxiv2024

SLC-25A46 Regulates Mitochondrial Fusion through FZO-1/Mitofusin and is Essential for Maintaining Neuronal Morphology

Mitochondria are dynamic organelles shaped by sequential fission and fusion events. The mitochondrial protein SLC25A46 has been identified as a causative gene for mitochondrial neuropathies. However, the function of SLC25A46 in mitochondrial morphogenesis remains controversial, with several reports suggesting it acts as a mitochondrial fission factor, while others propose it as a fusion factor. In this study, employing forward genetics, we identified slc-25A46, a Caenorhabditis elegans orthologue of human SLC25A46, as an essential factor for mitochondrial fusion. Suppressor mutagenesis screening revealed loss-of-function mutations in drp-1, a mitochondrial fission factor, as suppressors of slc-25A46. The phenotype of slc-25A46 mutants is similar to those of fzo-1 mutants, wherein the mitochondrial fusion factor Mitofusin is disrupted. Overexpressing FZO-1/Mitofusin mitigated mitochondrial defects in slc-25a46 mutants, indicating SLC-25A46 promotes fusion through FZO-1/Mitofusin. Disease model worms carrying mutations associated with SLC25A46 exhibited mitochondrial fragmentation and accelerated neurodegeneration, suggesting slc-25A46 maintains neuronal morphology through mitochondrial fusion regulation.

cell biology↗

bioRxiv2022

Germline-specific role for unconventional components of the γ-tubulin complex in Caenorhabditis elegans

The {gamma}-tubulin complex ({gamma}TuC) is a widely conserved microtubule nucleator, but some of its components GCP4-6. Here, we identified two {gamma}TuC-associated proteins in C. elegans, namely GTAP-1 and -2, for which apparent orthologs were detected only in the genus Caenorhabditis. Their centrosomal localization was interdependent. In early C. elegans embryos, whereas the conserved {gamma}TuC component MZT-1/MOZART1 was essential for the localization of centrosomal {gamma}-tubulin, depletion of GTAP-1 and/or -2 caused up to 50% reduction of centrosomal {gamma}-tubulin and precocious disassembly of spindle poles during mitotic telophase. In the adult germline, GTAP-1 and GTP-2 contributed to the efficient recruitment of {gamma}TuC to the plasma membrane. Depletion of GTAP-1, but not GTAP-2, severely disrupted both the microtubule array and the honeycomb-like structure in the adult germline. We propose that GTAP-1 and -2 are unconventional components of {gamma}TuC that contribute to the organization of both centrosomal and non-centrosomal microtubules by targeting the {gamma}TuC to specific subcellular sites in a tissue-specific manner. SUMMARY STATEMENTHaruta et al. show that GTAP-1 and -2, two unconventional components of the {gamma}-tubulin complex ({gamma}TuC) in C. elegans, contribute to targeting the {gamma}TuC to embryonic centrosomes and germ-cell membrane in adults.

cell biology↗

bioRxiv2022

Identification of lactic acid bacteria with reduced inflammatory and enhanced protective properties against influenza virus

Lactic acid bacteria (LAB) exert beneficial effects on health by regulating innate immunity in the intestinal tract. Many LAB that demonstrate anti-viral properties depend on the hosts inflammatory responses; however, a few LAB strains have low inflammatory and anti-viral properties. In this study, the LAB strain D279 (NITE_BP-03645, Latilactobacillus sakei) was isolated from among 741 LAB strains that were analyzed for their ability to induce interleukin 12 (IL-12), and was subsequently characterized. D279 induced the highest levels of IL-12 among the screened LAB. Further, D279 significantly activated anti-viral genes and preferentially induced IFN{lambda} in vitro, which plays a critical role in the epithelial tissue, conferring strong anti-influenza potency without inflammation, whereas IFN levels were relatively lower. Administration of pasteurized D279 to mice resulted in strong anti-influenza potency, including higher natural killer (NK) cell activity, and a reduced number of viruses in the lung compared to the control. Importantly, no D279-fed mice were sacrificed during the viral infection tests. Taken together, these results suggest that D279 administration confers beneficial effects with reduced inflammation, regulates innate immunity, and may be relevant for commercial use in the future.

microbiology↗

bioRxiv2021

The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans

The RNA polymerase II-associated factor 1 complex (PAF1C) is a protein complex that consists of LEO1, RTF1, PAF1, CDC73, and CTR9, and has been shown to be involved in Pol II-mediated transcriptional and chromatin regulation. Although it has been shown to regulate a variety of biological processes, the precise role of the PAF1C during germ line development has not been clarified. In this study, we found that reduction in the function of the PAF1C components, LEO-1, RTFO-1, PAFO-1, CDC-73, and CTR-9, in Caenorhabditis elegans affects cell volume expansion of oocytes. Defects in oogenesis were also confirmed using an oocyte maturation marker, OMA-1::GFP. While four to five OMA-1::GFP-positive oocytes were observed in wild-type animals, their numbers were significantly decreased in pafo-1 mutant and leo-1(RNAi), cdc-73(RNAi), and pafo-1(RNAi) animals. Expression of a functional PAFO-1::mCherry transgene in the germline significantly rescued the oogenesis-defective phenotype of the pafo-1 mutants, suggesting that expression of the PAF1C in germ cells is required for oogenesis. Notably, overexpression of OMA-1::GFP partially rescued the oogenesis defect in the pafo-1 mutants. Based on our findings, we propose that the PAF1C promotes oogenesis in a cell-autonomous manner by positively regulating the expression of genes involved in oocyte maturation.

developmental biology↗

bioRxiv2021

Centrosome maturation requires phosphorylation-mediated sequential domain interactions of SPD-5

Centrosomes consist of two centrioles and surrounding pericentriolar material (PCM). PCM expands during mitosis in a process called centrosome maturation, in which PCM scaffold proteins play pivotal roles to recruit other centrosomal proteins. In C. elegans, the scaffold protein SPD-5 forms PCM scaffold in a PLK-1 phosphorylation-dependent manner. However, how phosphorylation of SPD-5 promotes PCM scaffold assembly is unclear. Here, we identified three functional domains of SPD-5 through in vivo domain analyses, and propose that sequential domain interactions of SPD-5 are required for mitotic PCM scaffold assembly. Firstly, SPD-5 is targeted to centrioles through direct interaction between its centriole localization (CL) domain and a centriolar protein PCMD-1. Then, intra- and inter-molecular interaction between SPD-5 phospho-regulated multimerization (PReM) domain and the PReM association (PA) domain is triggered by phosphorylation by PLK-1, which leads to PCM scaffold expansion. Our findings suggest that the sequential domain interactions of scaffold proteins mediated by Polo/PLK-1 phosphorylation is an evolutionarily conserved mechanism of PCM scaffold assembly.

cell biology↗

bioRxiv2019

The first days in the life of naïve human B-lymphocytes infected with Epstein-Barr virus

Epstein-Barr virus (EBV) infects and activates resting human B-lymphocytes, reprograms them, induces their proliferation, and establishes a latent infection in them. In established EBV-infected cell lines many viral latent genes are expressed. Their roles in supporting the continuous proliferation of EBV-infected B cells in vitro are known, but their functions in the early, pre-latent phase of infection have not been investigated systematically. In studies during the first eight days of infection using derivatives of EBV with mutations in single genes of EBVs we found only EBNA2 to be essential for activating naive human B-lymphocytes, inducing their growth in cell volume, driving them into rapid cell divisions, and preventing cell death in a subset of infected cells. EBNA-LP, LMP2A and the viral microRNAs have supportive, auxiliary functions, but mutants of LMP1, EBNA3A, EBNA3C, and the noncoding EBER RNAs had no discernable phenotype compared with wild-type EBV. B cells infected with a double mutant of EBNA3A and 3C had an unexpected proliferative advantage and did not regulate the DNA damage response (DDR) of the infected host cell in the pre-latent phase. Even EBNA1 which has very critical long-term functions in maintaining and replicating the viral genomic DNA in established cell lines, was dispensable for the early activation of infected cells. Our findings document that the virus dose is a critical parameter and indicate that EBNA2 governs the infected cells initially and implements a strictly controlled temporal program independent of other viral latent genes. It thus appears that EBNA2 is sufficient to control all requirements for clonal cellular expansion and to reprogram human B-lymphocytes from energetically quiescent to activated cells.\n\nAuthor summaryThe preferred target of Epstein-Barr virus (EBV) are human resting B-lymphocytes. We found that their infection induces a well-coordinated, time-driven program that starts with a substantial increase in cell volume followed by cellular DNA synthesis after three days and subsequent rapid rounds of cell divisions on the next day accompanied by some DNA replication stress (DRS). Two to three days later the cells decelerate and turn into stably proliferating lymphoblast cell lines. With the aid of 16 different recombinant EBV strains we investigated the individual contributions of EBVs multiple latent genes during early B-cell infection and found that many do not exert a detectable phenotype or contribute little to EBVs pre-latent phase. The exception is EBNA2 that is essential in governing all aspects of B-cell reprogramming. EBV relies on EBNA2 to turn the infected B-lymphocytes into proliferating lymphoblasts preparing the infected host cell for the ensuing stable, latent phase of viral infection. In the early steps of B-cell reprogramming viral latent genes other than EBNA2 are dispensable but some, EBNA-LP for example, support the viral program and presumably stabilize the infected cells once viral latency is established.

microbiology↗

bioRxiv2018

A transgenic mutant mouse line accompanied by the complete deletion of interleukin-33 showed insulin and leptin resistances

Interleukin (IL) -33 has been identified as a member of the IL-1 family. Members of the IL-1 family have been reported to be involved in the regulation of energy homeostasis and glucose metabolism. Homozygous transgenic mutant mice of FLP14 line, that we previously generated, unexpectedly developed mature-onset obesity and diabetes. Through genetic investigations, we found that insertion of the transgenes had resulted in complete deletion of the Il33 gene. These obese male homozygous mutant mice exhibited hyperphagia with hyperleptinemia and insulin resistance caused by increased hepatic gluconeogenesis and decreased glucose uptake in skeletal muscle. As a result of examining preobese male homozygous mutant mice to investigate with the exclusion of the effect of obesity, hyperphagia with hyperleptinemina and insulin resistance caused by decreased glucose uptake in skeletal muscle were already observed, but the increased hepatic glucose production was not. To investigate whether the insulin resistance was caused by deletion of the Il33 gene, we treated these preobese homozygous mutant mice with recombinant IL-33 protein and noted a significant improvement in insulin resistance. Thus, insulin resistance in these homozygous mutant mice was caused, at least in part, by IL-33 deficiency, suggesting a favorable role of IL-33 for glucose metabolism in the skeletal muscle.

molecular biology↗