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Nakagawa, T.

Publications and source records attributed to Nakagawa, T..

At least 37 records · Page 2Linked to original sources

PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation

Spermatogonial stem cell functionality resides in the slow-cycling and heterogeneous undifferentiated spermatogonia cell population. This pool of cells supports lifelong fertility in adult males by balancing self-renewal and differentiation to produce haploid gametes. However, the molecular mechanisms underpinning long-term stemness of undifferentiated spermatogonia during adulthood remain unclear. Here, we discover that an epigenetic regulator, Polycomb repressive complex 1 (PRC1), shields adult undifferentiated spermatogonia from differentiation, maintains slow cycling, and directs commitment to differentiation during steady-state spermatogenesis in adults. We show that PRC2-mediated H3K27me3 is an epigenetic hallmark of adult undifferentiated spermatogonia. Indeed, spermatogonial differentiation is accompanied by a global loss of H3K27me3. Disruption of PRC1 impairs global H3K27me3 deposition, leading to precocious spermatogonial differentiation. Therefore, PRC1 directs PRC2-H3K27me3 deposition to maintain the self-renewing state of undifferentiated spermatogonia. Importantly, in contrast to its role in other tissue stem cells, PRC1 negatively regulates the cell cycle to maintain slow cycling of undifferentiated spermatogonia. Our findings have implications for how epigenetic regulators can be tuned to regulate the stem cell potential, cell cycle, and differentiation to ensure lifelong fertility in adult males.

developmental biology↗

FBXO24 ensures male fertility by preventing abnormal accumulation of membraneless granules in sperm flagella

Ribonucleoprotein (RNP) granules are membraneless electron-dense structures rich in RNAs and proteins, and involved in various cellular processes. Two RNP granules in male germ cells, intermitochondrial cement and the chromatoid body (CB), are associated with PIWI-interacting RNAs (piRNAs) and are required for transposon silencing and spermatogenesis. Other RNP granules in male germ cells, the reticulated body and CB remnants, are also essential for spermiogenesis. In this study, we disrupted FBXO24, a testis-enriched F-box protein, in mice and found numerous membraneless electron-dense granules accumulated in sperm flagella. Fbxo24 knockout (KO) mice exhibited malformed flagellar structures, impaired sperm motility, and male infertility, likely due to the accumulation of abnormal granules. The amount and localization of known RNP granule-related proteins were not disrupted in Fbxo24 KO mice, suggesting that the accumulated granules were distinct from known RNP granules. Further studies revealed that RNAs and two importins, IPO5 and KPNB1, abnormally accumulated in Fbxo24 KO spermatozoa and that FBXO24 could ubiquitinate IPO5. In addition, IPO5 and KPNB1 were recruited to stress granules, RNP complexes, when cells were treated with oxidative stress or a proteasome inhibitor. These results suggest that FBXO24 is involved in the degradation of IPO5, disruption of which may lead to the accumulation of abnormal RNP granules in sperm flagella.

developmental biology↗

Genetic and transcriptomic dissection of nitrate-independent function of Arabidopsis NRT1.1/NPF6.3/CHL1 under high ammonium condition

The Arabidopsis nitrate transceptor NRT1.1/NPF6.3/CHL1 regulates physiological responses to nitrate. Several studies have reported that Arabidopsis plants lacking NRT1.1 show enhanced shoot growth under toxic levels of ammonium without nitrate, suggesting a nitrate-independent function for NRT1.1. To further investigate this nitrate-independent function and its impact on ammonium tolerance, we conducted genetic analysis, tissue-specific expression analysis, and transcriptome analysis using various NRT1.1-related lines. Transgenic plants expressing either nonphosphomimic or phosphomimic mutants of NRT1.1 exhibited similar ammonium tolerance to the wild-type. The chl1-9 mutant, in which NRT1.1 with the P492L substitution is localized intracellularly rather than at the plasma membrane and fails to transport nitrate, showed significantly improved ammonium tolerance. Confocal imaging revealed that the NRT1.1-GFP signal was detected in the plasma membrane of various tissues, including cotyledon pavement cells, hypocotyl epidermal cells, mesophyll cells, root cap cells, and epidermal cells near root tips. In early seedlings, the absence of functional NRT1.1 altered the expression of genes associated with aliphatic glucosinolate biosynthesis, ethylene signaling, and low pH stress. Genes predicted to encode products localized to the extracellular space were enriched among those differentially expressed due to NRT1.1 deficiency. Our data suggest that in the absence of nitrate, plasma membrane-targeted NRT1.1 reduces ammonium tolerance irrespective of its phosphorylation state with alterations of gene expression associated with stress and senescence.

plant biology↗

Dimension reduction of microbiome data linked Bifidobacterium to allergic rhinitis

Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis (PCA), principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization (NMF), to a microbiome dataset from 186 subjects with symptoms of AR and 106 controls. All the dimension reduction methods supported that the enterotype clusters were overlapped in the dimension reduction plots, and that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed between the dimension reduction methods. The second composite variable calculated from PCoA was significantly associated with the intake of several nutrients, including omega-3 polyunsaturated fatty acids, and the risk of AR. The composite variable was also correlated with the relative abundance of Bifidobacterium, and thus, Bifidobacterium was related to the risk of AR and intake of several nutrients through dimension reduction. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.

microbiology↗

Isoxanthohumol improves obesity and glucose metabolism via inhibiting intestinal lipid absorption with a bloom of Akkermansia muciniphila in mice

AimsDysbiosis is an important factor that leads to metabolic disorders by disrupting energy balance and insulin sensitivity. A decrease in Akkermansia muciniphila is a phenotype of obesity-induced dysbiosis. Although interventions to increase A. muciniphila are expected to improve glucose metabolism, the underlying mechanism has not been fully understood. MethodsIsoxanthohumol (IX), a prenylated flavonoid found in beer hops was administered to high fat diet-fed mice. We analyzed glucose metabolism, gene expression profiles and histology of liver, epididymal adipose tissue and colon. Lipase activity, fecal lipid profiles and plasma metabolomic analysis were assessed. Fecal 16s rRNA sequencing was obtained and selected bacterial species were used for in vitro studies. Fecal microbiota transplantation and monocolonization were conducted to antibiotic-treated or germ-free (GF) mice. ResultsThe administration of IX lowered weight gain, decreased steatohepatitis and improved glucose metabolism. Mechanistically, IX inhibited pancreatic lipase activity and lipid absorption by decreasing the expression of the fatty acid transporter CD36 in the small intestine, which was confirmed by increased lipid excretion in feces. IX administration improved the gut barrier function and reduced metabolic endotoxemia. In contrast, the effects of IX were nullified by antibiotics. As revealed using 16S rRNA sequencing, the microbial community structure changed with a significant increase in the abundance of A. muciniphila in the IX-treated group. An anaerobic chamber study showed that IX selectively promoted the growth of A. muciniphila while exhibiting antimicrobial activity against some Bacteroides and Clostridium species. To further explore the direct effect of A. muciniphila on lipid and glucose metabolism, we monocolonized either A. muciniphila or Bacteroides thetaiotaomicron to GF mice. A. muciniphila monocolonization decreased CD36 expression in the jejunum and improved glucose metabolism, with decreased levels of multiple classes of fatty acids determined using plasma metabolomic analysis. ConclusionOur study confirmed a direct role of A. muciniphila in energy metabolism, which was induced by microbial actions of IX. These highlight new treatment strategies for preventing metabolic syndrome by boosting the gut microbiota with food components.

microbiology↗

EBF1 limits the numbers of cochlear hair and supporting cells and forms the scala tympani and spiral limbus during the development of the inner ear

Early B-cell factor 1 (EBF1) is a basic helix-loop-helix transcription factor essential for the differentiation of various tissues. Our single-cell RNA sequencing data suggest that Ebf1 is expressed in the sensory epithelium of the inner ear. Here, we found that the Ebf1 gene and its protein are expressed in the prosensory domain of the inner ear, medial region of the cochlear floor, inner ear mesenchyme, and cochleo-vestibular ganglion. Ebf1 deletion results in incomplete formation of the spiral limbus and scala tympani, increased number of cells in the organ of Corti and Kollikers organ, and aberrant course of the spiral ganglion axons. The inner ear-specific deletion of Ebf1 revealed that scala tympani formation depended on Ebf1 expressed in the otic mesenchyme. Ebf1 deletion in the cochlear epithelia caused the proliferation of SOX2-positive cochlear cells at E13.5, indicating that EBF1 suppresses the proliferation of the prosensory domain and cells of Kollikers organ to facilitate the development of appropriate numbers of hair and supporting cells. Furthermore, mice with deletion of cochlear epithelium-specific Ebf1 showed poor postnatal hearing function. Our results suggest that Ebf1 is essential for normal auditory function in mammals.

developmental biology↗

Scale space calibrates present and subsequent spatial learning in Barnes maze in mice

Animals including humans are capable of representing different scale spaces from smaller to larger ones. However, most laboratory animals live their life in a narrow range of scale spaces like home-cages and experimental setups, making it hard to extrapolate the spatial representation and learning process in large scale spaces from those in conventional scale spaces. Here, we developed a 3-meter diameter Barnes maze (BM3), then explored whether spatial learning in Barnes maze (BM) is calibrated by scale spaces. In the BM3, mice exhibited lower learning rate compared to a conventional 1-meter diameter Barnes maze (BM1), suggesting that the BM3 requires more trial-and-error and larger computational resources to solve the task than the BM1. Analyzing network structures of moving trajectories, betweenness centrality would contrast spatial learning in a larger scale space with that in a smaller one, as it diverges between the BM1 and the BM3 along with the learning progression. We then explored whether prior learning in either BM scale calibrates subsequent spatial learning in the other BM scale, and found asymmetric facilitation such that the prior learning in the BM3 facilitated the subsequent learning in the BM1, but not vice versa. Network structures of trajectories in the subsequent BM scale were changed by both prior and subsequent BM scale. These results suggest that scale space calibrates both the present and subsequent BM learning. This is the first study to explore and demonstrate scale-dependent spatial learning in Barnes maze in mice. Significance StatementAnimals are capable of representing different scale spaces. However, whether scale space calibrates goal-directed spatial learning remains unclear. The Barnes maze is a well-established experimental paradigm to evaluate spatial learning in rodents. Here, we developed a larger scale 3-meter diameter Barnes maze (BM3) then compared various navigation features in mice between the BM3 and a conventional 1-meter diameter Barnes maze (BM1). We demonstrated that learning on the BM3 required more computational resources than in the BM1, prompting mice to exploit unique navigation patterns. Such learning experiences in the BM3 facilitated subsequent spatial learning in the BM1, but not vice versa. These results suggest that scale space calibrates immediate and subsequent spatial learning.

animal behavior and cognition↗

A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter

In Kimoto-style fermentation, a fermentation starter is produced before the primary brewing process to stabilize fermentation. Nitrate-reducing bacteria, mainly derived from brewing water, produce nitrite, and lactic acid bacteria such as Leuconostoc can proliferate because of their tolerance towards low temperature and their low nutritional requirements. Later, Lactobacillus becomes the dominant genus, leading to weakly acidic conditions that contribute to control yeasts and undesired bacterial contaminants. However, the sources of these microorganisms that play a pivotal role in Sake brewing have not yet been revealed. Thus, comprehensive elucidation of the microbiome is necessary. In this study, we performed 16S rRNA amplicon sequencing analysis after sampling from floor, equipment surfaces, and raw materials for making fermentation starters, including koji, and water in Tsuchida Sake brewery, Gunma, Japan. Amplicon sequence variants (ASVs) between the external environments and the fermentation starter were compared, and it was verified that the microorganisms in the external environments, such as built environments, equipment surfaces, and raw materials in the sake brewery, were introduced into the fermentation starter. Furthermore, various adventitious microbes present in the fermentation starter of early days and from the external environments were detected in a nonnegligible proportion in the starter, which may impact the taste and flavor. These findings illuminate the uncharacterized microbial dark matter of sake brewing, the sources of microbes in Kimoto-style fermentation.

microbiology↗

Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics

AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP {gamma}8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-{gamma}8 receptor associated with three potent, chemically diverse drugs. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators.

neuroscience↗

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus.

The Kimoto-style fermentation starter is a traditional preparation method of sake brewing. In this process, specific microbial transition patterns have been observed within nitrate-reducing bacteria and lactic acid bacteria during the production process of the fermentation starter. We have characterized phylogenetic compositions and diversity of the bacterial community in a sake brewery performing the Kimoto-style fermentation. Comparing the time-series changes with other sake breweries previously reported, we found a novel type of Kimoto-style fermentation in which the microbial transition differed significantly from other breweries during the fermentation step. Specifically, the lactic acid bacteria, Leuconostoc spp. was a predominant species in the late stage in the preparation process of fermentation starter, on the other hand, Lactobacillus spp., which plays a pivotal role in other breweries, was not detected in this analysis. The discovery of this new variation of microbiome transition in Kimoto-style fermentation has further deepened our understanding of the diversity of sake brewing.

microbiology↗

Single-cell RNA-seq reveals stepwise fate conversion of supporting cells to hair cells in the chick auditory epithelium

In contrast to mammals, the avian cochlea, specifically the basilar papilla, can regenerate sensory hair cells, which involves fate conversion of supporting cells to hair cells. To determine the mechanisms for converting supporting cells to hair cells, we used single-cell RNA sequencing during hair cell regeneration in explant cultures of chick basilar papillae. We identified dynamic changes in the gene expression of supporting cells, and the pseudotime trajectory analysis demonstrated the stepwise fate conversion from supporting cells to hair cells. Initially, supporting cell identity was erased and transition to the precursor state occurred. A subsequent gain in hair cell identity progressed together with downregulation of precursor-state genes. Transforming growth factor beta receptor 1-mediated signaling was involved in induction of the initial step, and its inhibition resulted in suppression of hair cell regeneration. Our data provide new insights for understanding fate conversion from supporting cells to hair cells in avian basilar papillae.

neuroscience↗

Root-specific activation of plasma membrane H+-ATPase 1 enhances plant growth and shoot accumulation of nutrient elements under nutrient-poor conditions in Arabidopsis thaliana

Plasma membrane (PM) H+-ATPase contributes to nutrient uptake and stomatal opening by creating proton gradient across the membrane. Previous studies report that a dominant mutation in the OPEN STOMATA2 locus (OST2-2D) constitutively activates Arabidopsis PM H+-ATPase 1 (AHA1), which enlarges proton motive force for root nutrient uptake. However, the stomatal opening is also constitutively enhanced in the ost2-2D, causing drought hypersensitivity. To develop plants with improved nutrient acquisition and normal stomatal movement, we generated grafted plants (scion/rootstock : Col-0 (WT)/ost2-2D), and compared their growth and nutrient element content with those of control plants (WT/WT) under two nutrient regimes. WT/ost2-2D shoots had larger weights, rosette diameter, leaf blade area, and content of C, N, K, Ca, S, P, Mg, Na, Mn, B, Co, and Mo under nutrient-poor conditions compared with WT/WT shoots. The root weights and primary root length were greater in WT/ost2-2D plants than in WT/WT plants under both nutrient conditions. These results suggest that root-specific activation of PM H+-ATPase enhances root nutrient uptake, which accelerates the plant growth under nutrient-poor condition. Our study presents a novel approach to improving nutrient uptake efficiency in crops and vegetable for the implementation of low-input sustainable agriculture.

plant biology↗

Multiple nutritional and gut microbial factors associated with allergic rhinitis: the Hitachi Health Study

Several studies suggest the involvement of dietary habits and gut microbiome in allergic diseases. However, little is known about the nutritional and gut microbial factors associated with the risk of allergic rhinitis (AR). We recruited 186 apparently healthy workers with symptoms of AR and 106 controls at the Hitachi Health Care Center, Japan. The habitual consumption of 42 selected nutrients were examined using the brief-type self-administered diet history questionnaire. Faecal samples were collected and subjected to amplicon sequencing of the 16S ribosomal RNA gene hypervariable regions. Association analysis revealed that four nutrients (retinol, vitamin A, cryptoxanthin, and copper) were negatively associated with AR. Among 40 genera examined, relative abundance of Prevotella and Escherichia were associated with AR. Furthermore, significant statistical interactions were observed between retinol and Prevotella. The age- and sex-adjusted odds of AR were 25-fold lower in subjects with high retinol intake and high Prevotella abundance compared to subjects with low retinol intake and low Prevotella abundance. Our data provide insights into complex interplay between dietary nutrients, gut microbiome, and the development of AR.

microbiology↗

Root-specific reduction of cytokinin perception enhances shoot growth with an alteration of trans-zeatin distribution in Arabidopsis thaliana

Compelling evidence demonstrates that root-derived cytokinins (CKs) contribute to shoot growth via long-distance transport; therefore, we hypothesized that an increase in root-derived CKs enhances shoot growth. To demonstrate this, we grafted Arabidopsis Col-0 (WT) scion onto rootstock originated from WT or a double-knockout line of CK receptors AHK2 and AHK3 (ahk23) because the knockout line over accumulates CKs in the body due to feedback homeostasis regulation. The grafted plants (scion/rootstock: WT/WT and WT/ahk23) were grown in vermiculite pots or solid media under high and low nitrogen regimes for vegetative growth and biochemical analysis. The root-specific deficiency of AHK2 and AHK3 increased root concentrations of trans-zeatin (tZ)-type and N6-({Delta}2-isopentenyl) adenine (iP)-type CKs, induced CK biosynthesis genes, and repressed CK degradation genes in the root. Shoot growth, shoot concentrations of tZ-type CKs, and shoot expression of CK-inducible marker genes were consistently larger in the WT/ahk23 plants than in the WT/WT plants. Moreover, the root-specific deficiency of AHK2 and AHK3 enhanced shoot growth in the WT scion more strongly than in the ahk23 scion. Given that tZ-type CKs are predominantly produced from iP-type CKs in the root and xylem-mobile, it is concluded that the root-specific reduction of CK perception would enhance shoot growth by increasing the amount of root-derived tZ-type CKs and their perception by the shoot. This study will present a novel approach to improve plant growth and productivity.

plant biology↗

An ancestral function of strigolactones as symbiotic rhizosphere signals

In flowering plants, carotenoid-derived strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), a previously unidentified SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating that it is ancestral in land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone.

plant biology↗

CCR4 blockade leads to clinical activity and prolongs survival in a canine model of advanced prostate cancer

Targeting regulatory T cell (Treg) infiltration is an emerging strategy for cancer immunotherapy. However, the efficacy of this strategy in advanced prostate cancer remains unclear. Here, we describe the therapeutic efficacy of this strategy in a canine model of advanced prostate cancer. We used dogs with naturally occurring prostate cancer to study the molecular mechanism underlying Treg infiltration into tumor tissues and the effect of anti-Treg treatment. We found that tumor-infiltrating Tregs were associated with poor prognosis in dogs bearing spontaneous prostate cancer. RNA sequencing and protein analyses showed that Treg infiltration was mediated by interaction between the tumor-producing chemokine, CCL17, and the receptor CCR4 expressed on Tregs. Dogs with advanced prostate cancer responded to mogamulizumab, a monoclonal antibody targeting CCR4, with improved survival and low incidence of clinically relevant adverse events. Exploratory analyses showed urinary CCL17 concentration and BRAFV595E mutation to be independently predictive of the response to mogamulizumab. Analysis of a publicly available transcriptomic dataset of human prostate cancer showed that the CCL17/CCR4 axis correlated with the Treg marker, Foxp3. In silico survival analyses showed that high expression of CCL17 was associated with poor prognosis. Immunohistochemistry confirmed that tumor-infiltrating Tregs expressed CCR4 in human patients with prostate cancer. These findings suggest that anti-Treg treatment through the blocking of CCR4 is a promising therapeutic approach for advanced prostate cancer. One Sentence SummaryTargeting regulatory T cell infiltration by CCR4 blockade induces objective responses and improves survival in a canine model of prostate cancer.

cancer biology↗

Fission yeast Rad8/HLTF facilitates Rad52-dependent chromosomal rearrangements through PCNA lysine 107 ubiquitination

Rad52 recombinase can cause gross chromosomal rearrangements (GCRs). However, the mechanism of Rad52-dependent GCRs remains unclear. Here, we show that fission yeast Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) of PCNA, a DNA sliding clamp. Loss of Rad8 reduced isochromosomes resulting from centromere inverted repeat recombination. Rad8 HIRAN and RING finger mutations reduced GCRs, suggesting that Rad8 facilitates GCRs through 3 DNA-end binding and ubiquitin ligase activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating proteins were required for GCRs. Consistent with this, PCNA K107R but not K164R mutation greatly reduced GCRs. Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, rad8, and rad52 mutations epistatically reduced GCRs. Remarkably, K107 is located at the interface between PCNA subunits, and an interface mutation D150E bypassed the requirement of PCNA K107 ubiquitination for GCRs. This study uncovers the role of Rad8-dependent PCNA K107 ubiquitination in Rad52-dependent GCRs.

genomics↗

EXOC1 regulates cell morphology of spermatogonia and spermatocytes in mice

Spermatogenesis requires high regulation of germ cell morphology. The spermatogonia regulates its differentiation state by its own migration. The male germ cells differentiate and mature with the formation of syncytia, failure of forming the appropriate syncytia results in the arrest of spermatogenesis at the spermatocyte stage. However, the detailed molecular mechanisms of male germ cell morphological regulation are unknown. Here, we found that EXOC1 is important for the pseudopod formation of spermatogonia and spermatocyte syncytia in mice. We found that while EXOC1 contributes to the inactivation of Rac1 in the pseudopod formation of spermatogonia, in spermatocyte syncytium formation, EXOC1 and SNAP23 cooperate with STX2. Our results showed that EXOC1 functions in concert with various cell morphology regulators in spermatogenesis. Since EXOC1 is known to bind to several cell morphogenesis factors, this study is expected to be the starting point for the discovery of many morphological regulators of male germ cells.

developmental biology↗