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Adachi, H.

Publications and source records attributed to Adachi, H..

At least 19 recordsLinked to original sources

Evolution of an unstable sex determination system in white Guinea yam (Dioscorea rotundata)

Plants often produce unstable sex phenotypes; however, the underlying evolutionary and molecular mechanisms are unclear. In white Guinea yam (Dioscorea rotundata), the most economically important tuber crop, genetic improvement is critical for food security but remains constrained by dioecy and complex sex phenotypes. White Guinea yam has a ZZ/ZW sex determination system in which ZZ individuals are consistently male, whereas ZW individuals can be female, male, or monoecious. Here we show that chromosome 11 is the sex chromosome, featuring a 1.2-Mb inversion between the Z and W chromosomes. A 170-kb W-specific region carries the microRNA gene dro-MIR432, likely involved in sex switching. The recent emergence of this miRNA-mediated ZZ/ZW system, distinct from the XY/XX system within Dioscorea, underscores the dynamic evolution of plant sex determination.

plant biology↗

Pseudouridines in the U2 Branch Site Recognition Region Differentially Contribute to Branch Site Recognition during Pre-mRNA Splicing

Pseudouridines ({Psi}s) are highly enriched in conserved, functionally critical regions of spliceosomal snRNAs, particularly within the U2 branch site recognition region (BSRR), which contains six {Psi}s in humans and three in S. cerevisiae. To investigate how U2 BSRR pseudouridylation influences branch site sequence (BSS) recognition, we developed a large-scale, high-throughput screening system in S. cerevisiae that allows a library of pre-mRNAs with randomized BSSs to be spliced in distinct U2 BSRR pseudouridylation backgrounds. Screening and next-generation sequencing (NGS) revealed that different U2 pseudouridylation backgrounds exhibit distinct recognition patterns and efficiencies for specific BSSs. Notably, {Psi}42 and {Psi}44 generally enhanced splicing, whereas {Psi}38 alone, and in some contexts together with {Psi}35, consistently impaired BSS recognition. The differential effects were validated using endogenous S. cerevisiae genes. In addition, splicing assays with engineered pre-mRNA constructs guided by the screening results demonstrated that BSRR {Psi}s directly influence BSS selection, supporting a model in which U2 pseudouridylation modulates BSS recognition and could contribute to alternative splicing in more complex eukaryotes. Finally, synthetic-lethality analyses with a Prp5 mutant, together with Prp5-U2-pre-mRNA binding assays, indicate that U2 BSRR {Psi}s are critical for Prp5 recruitment and, consequently, for proper U2-BSS interactions during spliceosome assembly. Collectively, these findings establish U2 pseudouridylation as a key determinant of branch site recognition and spliceosome function.

molecular biology↗

Morphogenesis of the Carapace from Phyllosoma to Puerulus in Spiny Lobsters

Molting in exoskeleton-bearing organisms can result in dramatic body shape transformations. While this phenomenon has been well-studied in insects, limited knowledge exists for other taxa, including crustaceans. Among crustaceans, achelatan lobsters, such as Palinuridae and Scyllaridae, exhibit a unique metamorphic transition from a flattened phyllosoma larva to a three-dimensional puerulus or nisto larva in a single molt. This study investigates the mechanisms underlying this transformation, focusing on carapace deformation through histological analysis, live imaging, and computational modeling. Three-dimensional micro-computed tomography revealed a significant reduction in body length during metamorphosis. Live imaging captured dynamic morphological changes, including epithelial contraction and subsequent reshaping. Scanning electron microscopy identified a distinctive furrow structure on the carapace surface, absent in post-molt puerulus larvae, suggesting a role in the transformation process. To explore the formation of this furrow pattern, a computational model was developed based on differential shrinkage rates in vertical and horizontal directions. The model successfully reproduced similar patterns observed in natural specimens, implying that controlled anisotropic contraction could contribute to morphogenesis. Furthermore, three-dimensional shrinkage simulations demonstrated that local contraction with constrained out-of-plane deformation can generate folds, which later expand to form curved structures. This study provides novel insights into the biomechanics of arthropod molting, highlighting a previously unrecognized mechanism of two-dimensional-to-three-dimensional transformation. The findings enhance our understanding of achelatan lobster development and offer broader implications for exoskeletal morphogenesis across arthropods.

developmental biology↗

Calcium-dependent protein kinases participate in RBOH-mediated sustained ROS burst during plant immune cell death

The sensing of pathogen effector by an intracellular receptor called nucleotide-binding leucine-rich repeat receptor (NLR), induces a robust immune response, effector-triggered immunity (ETI). Sustained reactive oxygen species (ROS) production is accomplished by Nicotiana benthamiana RBOHB, an NADPH oxidase. However, molecular mechanisms connecting effector recognition and ROS production are unclear. Here, we show that calcium-dependent protein kinases (CDPKs) contribute to sustained ROS production downstream of NLR activation. We found that NbCDPK4 and NbCDPK5 directly phosphorylate NbRBOHB Ser-123 and provokes ROS production. In addition, constitutively active NbCDPKs upregulated NbRBOHB transcription. The phosphorylation of Ser-123 was significantly increased in a Ca2+-dependent manner during the ETI-like responses, which execute hypersensitive cell death. Moreover, transient expression of an autoactive helper NLR, NRC4, induced phosphorylation of Ser-123 dependent on its N-terminal conserved motif required for Ca2+ channel activity. These findings uncover a critical role for the NbCDPK-NbRBOHB module in regulating sustained ROS production during ETI.

plant biology↗

Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro

Dioecious plants, which have distinct male and female individuals, constitute [~]5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we describe the molecular basis of sex determination in the monocot Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex determination (XY) system, with sex determination regions located on chromosome 3. Sequence read coverage analysis of the sex chromosomes revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we identified two candidate genes that are likely involved in sex determination: BLH9, encoding a homeobox protein, and HSP90, encoding a molecular chaperone. BLH9 has similar functions to AtBLH9 in Arabidopsis thaliana. BLH9 is thought to suppress female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants. Author summarySexual reproduction is a nearly universal, indispensable feature of evolution in eukaryotes. The molecular mechanisms underlying sex determination vary depending on the taxon. However, most information about this process was derived from studies of model organisms and/or domesticated species. To elucidate the diversity and evolution of sex determination, we need to expand the taxonomic breadth of these investigations. Here, we focused on the monocot genus Dioscorea, which contains species with multiple sex-determination systems, suggesting that frequent evolutionary transitions occur between the different sex-determination systems. We investigated the genetics of sex determination in Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Whole-genome assembly and genetic analysis, along with transcriptome analysis, suggested that this species employs a male heterogametic sex determination (XY) system, with two Y-chromosome-specific genes that might be involved in male and female differentiation. These findings enhance our understanding of the complex evolution of dioecy.

plant biology↗

A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs

Nucleotide-binding domain and leucine-rich repeat immune receptors (NLRs) are known for their rapid evolution, even at the intraspecific level, yet the rates of evolution differ significantly across various NLR classes. Within the NRC (NLR Required for Cell Death) network, NLRs operate in complex sensor-helper configurations to confer immunity against a diverse array of pathogens, particularly in Asterids. While helper NLRs are typically conserved and evolve slowly, sensor NLRs tend to evolve more rapidly. However, the functional connections between slow and fast-evolving NLRs remain poorly understood, notably in important crop species. We conducted a comparative analysis of NLRs across 40 Solanales and 29 Asterales genomes to explore NRC network expansion and diversification within the less-studied Asterales order. Our findings reveal that the NRC network has expanded less in Asterales compared to Solanales. We functionally validated a minimal Asterales NRC network with 2 helpers and 9 sensors in common lettuce (Lactuca sativa). Through selection and diversification analysis and structural modeling of NRC helper and sensor subclades in the Lactuca genus, we found varying evolutionary diversification rates between NRC helpers and sensors. We found a correlation between sensor diversification rates and helper dependency, with sensors reliant on a phylogenetically conserved helpers experiencing limited diversification pressure. Our results highlight the lineage- and function-specific evolution of the NRC network, offering insights into the evolutionary pressures shaping plant immune receptor networks.

plant biology↗

Epigenetic Control of TERRA by FTSJ3 is Critical for Telomerase-Driven Cancers

Telomerase reverse transcriptase (hTERT) overexpression, a hallmark of most cancers, drives tumorigenesis by enabling limitless replicative potential. Direct targeting of hTERT is challenging, necessitating alternative strategies. Through genome-wide synthetic dosage lethality (SDL) screening in cancer models, including patient-derived organoids, we identify FTSJ3, an RNA 2-O-methyltransferase, as a critical vulnerability in hTERT-overexpressing cells. FTSJ3 methylates telomeric repeat-containing RNA (TERRA), a modification essential for recruiting SUV39H1 to telomeric ends to mediate H3K9 trimethylation and establish stable heterochromatin. Loss of FTSJ3 disrupts this cascade, impairing H3K9 trimethylation, HP1-alpha recruitment, and telomeric heterochromatin maintenance. Notably, this reveals an unexpected dependency on TERRA methylation for telomeric heterochromatin stability in hTERT-driven cancers. Non-malignant cells, lacking telomerase activity and de novo telomere repeat synthesis, are unaffected by FTSJ3 suppression. Our findings establish the FTSJ3/TERRA/SUV39H1 axis as a critical mechanism supporting telomeric heterochromatin stability in hTERT-driven cancers. This telomere-directed epigenetic strategy provides a robust framework for translational therapeutic innovation.

cancer biology↗

Post-embryonic tail development through molting of the freshwater shrimp Neocaridina denticulata

BackgroundUnderstanding postembryonic morphogenesis through molting in arthropods has recently become a focus of developmental biology. The hierarchical mechanisms of epithelial sheet folds play a significant role in this process. Drosophila is a well-studied model for holometabolous insects, with extensive research on imaginal disc growth. While developmental processes in other arthropods have been described, live imaging of morphological changes is challenging due to the macroscopic movements and hard cuticles. Neocaridina denticulata, a crustacean, presents unique tail morphogenesis through molting, which makes it the potential model. This study investigated the development of the tail in Neocaridina denticulata through histological analysis and in vivo live imaging using fluorescent probes. This study also performed long-read sequencing of the whole genome for future genetic tools. ResultsThe tail of Neocaridina was found to undergo two major changes with the first ecdysis. Firstly, the branches of the uropods are cleared, and secondly, the telson undergoes convergent elongation. Cross-sectional analysis revealed that uropod and telson branching occurs immediately after hatching in the form of cuticle branching. The surface structure of the developmental tail suggested that telson elongation is achieved by the extension of anisotropic furrows in the cuticle during ecdysis. Anisotropy of cuticle furrows was associated with the epithelial cell shape, and the anisotropy of cell shape was found to occur during development from post-hatching. We also established an in vivo live imaging system with UV-LED resin and detected the changes of tail development over time. in vivo live imaging analysis revealed that telson contraction occurs gradually prior to ecdysis. Furthermore, we have also provided a draft genome of Neocaridina. ConclusionNeocaridina denticulata is a valuable model for studying morphogenesis in arthropods through molting. The tail undergoes complex changes involving cuticle branching, anisotropic furrows, and cellular dynamics. in vivo live imaging system provides insights into the developmental process, and the draft genome enhances the potential for genetic tools in future studies. This research contributes to the understanding of arthropod morphogenesis and provides a foundation for further developmental and cytological investigations in Neocaridina.

developmental biology↗

A root-specific NLR network confers resistance to plant parasitic nematodes

Nucleotide-binding domain and leucine-rich repeat immune receptors (NLRs) confer disease resistance to a multitude of foliar and root parasites of plants. However, the extent to which NLR immunity is expressed differentially between plant organs is poorly known. Here, we show that a large cluster of tomato genes, which encodes the cyst and root-knot nematode disease resistance proteins Hero and MeR1 as well as the NLR-helper NRC6, exhibits nearly exclusive expression in the roots. This root-specific gene cluster emerged in Solanum species about 21 million years ago through gene duplication from the ancient NRC network of asterid plants. NLR-sensors in this gene cluster exclusively signal through NRC6 helpers to trigger the hypersensitive cell death immune response. These findings indicate that the NRC6 gene cluster has sub-functionalized from the larger NRC network to specialize for resistance against root pathogens, including cyst and root-knot nematodes. We propose that NLR gene clusters and networks have evolved organ-specific gene expression as an adaptation to particular parasites and to reduce the risk of autoimmunity.

plant biology↗

The nucleotide binding domain of NRC-dependent disease resistance proteins is sufficient to activate downstream helper NLR oligomerization and immune signaling

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins with pathogen sensor activities have evolved to initiate immune signaling by activating helper NLRs. However, the mechanisms underpinning helper NLR activation by sensor NLRs remain poorly understood. Although coiled-coil (CC) type sensor NLRs such as the Potato virus X disease resistance protein Rx have been shown to activate the oligomerization of their downstream helpers NRC2 and NRC4, the domains involved in sensor-helper signaling are not known. Here, we show that the nucleotide binding (NB) domain within the NB-ARC of the Potato virus X disease resistance protein Rx is necessary and sufficient for oligomerization and immune signaling of downstream helper NLRs. In addition, the NB domains of the disease resistance proteins Gpa2 (cyst nematode resistance), Rpi-amr1, Rpi-amr3 (oomycete resistance) and Sw-5b (virus resistance) are also sufficient to activate their respective downstream NRC helpers. Moreover, the NB domain of Rx and its helper NRC2 form a minimal functional unit that can be transferred from solanaceous plants (lamiids) to the Campanulid species lettuce (Lactuca sativa). Our results challenge the prevailing paradigm that NLR proteins exclusively signal via their N-terminal domains and reveal a signaling activity for the NB domain of NRC-dependent sensor NLRs. We propose a model in which helper NLRs monitor the status of the NB domain of their upstream sensors.

plant biology↗

The NRC0 gene cluster of sensor and helper NLR immune receptors is functionally conserved across asterid plants

NLR (nucleotide-binding domain and leucine-rich repeat-containing) proteins can form complex receptor networks to confer innate immunity. NRCs are phylogenetically related nodes that function downstream of a massively expanded network of disease resistance proteins that protect against multiple plant pathogens. Here, we used phylogenomic methods to reconstruct the macroevolution of the NRC family. One of the NRCs, we termed NRC0, is the only family member shared across asterid plants, leading us to investigate its evolutionary history and genetic organization. In several asterid species, NRC0 is genetically clustered to other NLRs that are phylogenetically related to NRC-dependent disease resistance genes. This prompted us to hypothesize that the ancestral state of the NRC network is an NLR helper-sensor gene cluster that was present early during asterid evolution. We validated this hypothesis by demonstrating that NRC0 is essential for the hypersensitive cell death induced by its genetically linked sensor NLR partners in four divergent asterid species: tomato, wild sweet potato, coffee and carrot. In addition, activation of a sensor NLR leads to high-order complex formation of its genetically linked NRC0 similar to other NRCs. Our findings map out contrasting evolutionary dynamics in the macroevolution of the NRC network over the last 125 million years from a functionally conserved NLR gene cluster to a massive genetically dispersed network. One-sentence summaryNRC0 gene cluster is functionally conserved across divergent asterid species and predates the massively expanded NRC network.

plant biology↗

Mechanical models affecting beetle horn remodeling

Clarifying the mechanisms of shape alteration by insect metamorphosis is important for comprehending exoskeletal morphogenesis. The large horn of the Japanese rhinoceros beetle Trypoxylus dichotomus is the result of drastic metamorphosis, wherein it appears as a rounded shape via pupation and then undergoes remodeling into an angular adult shape. However, the mechanical mechanisms of this remodeling process remain unknown. In this study, we investigated the remodeling mechanisms of the Japanese rhinoceros beetle horn by developing a physical simulation. We identified three factors contributing to remodeling by biological experiments--ventral adhesion, uneven shrinkage, and volume reduction--which were demonstrated to be crucial to the transformation by a physical simulation. We also corroborated our findings by applying the simulation to the stag beetles mandibular remodeling. These results indicate that the physical simulation is applicable to pupal remodeling in other beetles, and the morphogenic mechanisms could explain various exoskeletal shapes. Significance statementThe metamorphosis in insects is a mysterious process. By metamorphosis, insects sometimes change their shape dramatically. The head horn of the Japanese rhinoceros beetle is one of the most famous examples of metamorphosis. In larva-to-pupa molting, the horn appears suddenly, caused by the "furrow formation and unfolding" mechanism. The unfolding process makes the pupal horn rounded. However, pupa-to-adult molting transforms the rounded shape into an angular shape. In this paper, we investigated the mechanisms of the transformation. We extracted factors contributing to it through observations and experiments and developed a physical simulation. It could reproduce the adult shape from the pupal shape and could be a general model for the pupa-adult transformation of beetles.

developmental biology↗

Discrimination of SARS-CoV-2 Omicron sub-lineages BA.1 and BA.2 using a high-resolution melting-based assay: A pilot study

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. As of March 2022, Omicron variant BA.2 is rapidly replacing variant BA.1. As variant BA.2 may cause more severe disease than variant BA.1, variant BA.2 requires continuous monitoring. The current study aimed to develop a novel high-resolution melting (HRM) assay for variants BA.1 and BA.2 and to determine the sensitivity and specificity of our method using clinical samples. Here, we focused on the mutational spectra at three regions in the spike receptor-binding domain (RBD; R408, G446/L452, and S477/T478) for the variant-selective HRM analysis. Each variant was identified based on the mutational spectra as follows: no mutations (Alpha variant); L452R and T478K (Delta variant); G446S and S477N/T478K (Omicron variant BA.1); and R408S and S477N/T478K (Omicron variant BA.2). Upon analysis of mutation-coding RNA fragments, the melting peaks of the wild-type fragments were distinct from those of the mutant fragments. The sensitivity and specificity of this method were determined as 100% and more than 97.5%, respectively, based on 128 clinical samples (40 Alpha, 40 Delta, 40 Omicron variants BA.1/BA.1.1, and 8 Omicron BA.2). These results suggest that this HRM-based assay is a promising screening method for monitoring the transmission of Omicron variants BA.1 and BA.2.

microbiology↗

Self-organization, quality control, and preclinical studies of human iPSC-derived retinal sheets for tissue-transplantation therapy

Three-dimensional retinal organoids (3D-retinas) are a promising graft source for transplantation therapy. We previously developed self-organizing culture for 3D-retina generation from human pluripotent stem cells (hPSCs). Here we present a quality control method and preclinical studies for tissue-sheet transplantation. Self-organizing hPSCs differentiated into both retinal and off-target tissues. Gene expression analyses identified the major off-target tissues as eye-related, cortex-like, and spinal cord-like tissues. For quality control, we developed a qPCR-based test in which each hPSC-derived neuroepithelium was dissected into two tissue-sheets: inner-central sheet for transplantation and outer-peripheral sheet for qPCR to ensure retinal tissue selection. During qPCR, tissue-sheets were stored for 3-4 days using a newly developed preservation method. In a rat tumorigenicity study, no transplant-related adverse events were observed. In retinal degeneration model rats, retinal transplants differentiated into mature photoreceptors and exhibited light responses in electrophysiology assays. These results demonstrate our rationale toward self-organizing retinal sheet transplantation therapy.

neuroscience↗

Considering decoupled phenotypic diversification between ontogenetic phases in macroevolution: An example using Triggerfishes (Balistidae)

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that do not reflect the same traits as their adult forms. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. However, whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. Integrating a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, we reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.

evolutionary biology↗

An atypical NLR protein modulates the NRC immune receptor network

The NRC immune receptor network has evolved in asterid plants from a pair of linked genes into a genetically dispersed and phylogenetically structured network of sensor and helper NLR (nucleotide-binding domain and leucine-rich repeat-containing) proteins. In some species, such as the model plant Nicotiana benthamiana and other Solanaceae, the NRC network forms up to half of the NLRome, and NRCs are scattered throughout the genome in gene clusters of varying complexities. Here, we describe NRCX, an atypical, but essential member of the NRC family that lacks canonical features of these NLR helper proteins, such as a functional N-terminal MADA motif and the capacity to trigger autoimmunity. In contrast to other NRCs, systemic gene silencing of NRCX markedly impairs plant growth resulting in a dwarf phenotype. Remarkably, dwarfism of NRCX silenced plants is partially dependent on NRCX paralogs NRC2 and NRC3, but not NRC4. Despite its negative impact on plant growth when silenced systemically, transient RNA interference of NRCX in mature N. benthamiana leaves doesnt result in visible cell death phenotypes. However, alteration of NRCX expression modulates the hypersensitive response mediated by NRC2 and NRC3 in a manner consistent with a negative role for NRCX in the NRC network. We conclude that NRCX is an atypical member of the NRC network that has evolved to contribute to the homeostasis of this genetically unlinked NLR network.

plant biology↗

The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4

Cell surface pattern recognition receptors (PRRs) activate immune responses that can include the hypersensitive cell death. However, the pathways that link PRRs to the cell death response are poorly understood. Here, we show that the cell surface receptor-like protein Cf-4 requires the intracellular nucleotide-binding domain leucine-rich repeat containing receptor (NLR) NRC3 to trigger a confluent cell death response upon detection of the fungal effector Avr4 in leaves of Nicotiana benthamiana. This NRC3 activity requires an intact N-terminal MADA motif, a conserved signature of coiled-coil (CC)-type plant NLRs that is required for resistosome-mediated immune responses. A chimeric protein with the N-terminal 1 helix of Arabidopsis ZAR1 swapped into NRC3 retains the capacity to mediate Cf-4 hypersensitive cell death. Pathogen effectors acting as suppressors of NRC3 can suppress Cf-4-triggered hypersensitive cell-death. Our findings link the NLR resistosome model to the hypersensitive cell death caused by a cell surface PRR.

plant biology↗

Rpi-amr3 confers resistance to multiple Phytophthora species by recognizing a conserved RXLR effector

Diverse pathogens from the genus Phytophthora cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) proteins, that recognize RXLR effectors. However, whether NLR proteins can recognize RXLR effectors from multiple different Phytophthora pathogens has rarely been investigated. Here, we report the effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from S. americanum. We show here that AVRamr3 is broadly conserved in many different Phytophthora species, and that recognition of AVRamr3 homologs enables resistance against multiple Phytophthora pathogens, including P. parasitica and P. palmivora. Our findings suggest a novel path to identifying R genes against important plant pathogens.

plant biology↗