Biology subjects

Nishio, S.

Publications and source records attributed to Nishio, S..

8 recordsLinked to original sources

bioRxiv2026

How a single sperm protein recognizes highly divergent egg coat components

For successful fertilization, sperm must recognize and penetrate the egg coat, called vitelline envelope (VE) or, in mammals, zona pellucida (ZP). In abalone, sperm acrosomal protein lysin dissolves the VE by binding the N-terminal region of egg coat subunit VERL, encompassing 22 ZP-N domains (VR1-22), but how sperm engages other VE components remains unclear. Here we report free and lysin-bound structures of VEZP14-N1, the single ZP-N repeat of VERL paralog VEZP14, together with biochemical and biophysical data. Despite [~]20% sequence identity to VRs, VEZP14-N1 presents a structurally equivalent surface to lysin, indicating that conserved interaction geometry underlies recognition. Binding is asymmetric: lysin is conformationally rigid, whereas VEZP14-N1 requires homodimer dissociation and induced-fit rearrangements to bind -- kinetic costs that limit affinity to an intermediate level, consistent with a decoy role sequestering lysin from VERL. These findings illuminate how one sperm protein binds divergent egg coat targets, with implications for ZP-N repeat function in vertebrate gamete recognition.

biophysics↗

bioRxiv2026

FGFR1-phosphate sensing and crystal-induced gasdermin D signaling in neutrophils drive vascular calcification in CKD

Chronic kidney disease (CKD) confers disproportionate cardiovascular risk. In non-dialysis CKD, calcification accumulates primarily within the intimal layer. Clinical studies indicate that intimal calcification correlates with hyperphosphatemia, yet the cellular and molecular pathways remain unclear. Given evidence that osteocytes sense phosphate via fibroblast growth factor receptor 1 (FGFR1), we hypothesized that FGFR1-expressing vascular immune cells, especially neutrophils, act as mediators linking high phosphate to plaque mineralization. In vitro, phosphate triggered FGFR1-dependent signaling in human and murine neutrophils, inducing neutrophil extracellular traps (NETs). Activated neutrophils promoted the depletion of Fetuin-A, a major inhibitor of calcium-phosphate complexation, creating a milieu permissive to mineral nucleation. Newly formed calcium-phosphate particles amplified NETs through gasdermin D (GSDMD), establishing a feed-forward loop that enhanced mineralization and endothelial injury in co-culture assays. Human arteriosclerotic plaques from CKD patients showed NETs markers co-localizing with calcified deposits. In vivo, pharmacological FGFR inhibition attenuated arterial intimal calcification and suppressed NET formation in CKD mice. These findings identify phosphate sensing via neutrophil FGFR1 and subsequent crystal-induced GSDMD signaling as drivers of intimal vascular calcification in CKD. Targeting phosphate-sensing pathways, NET formation, and neutrophil-driven mineralization may mitigate vascular calcification and reduce cardiovascular risk in CKD.

immunology↗

bioRxiv2026

YY1 Binding Motif at Upstream of Rep/Cap Increases AAV Yield and Full Capsids

Adeno-associated virus (AAV) vectors are widely used in gene therapy, whereas low manufacturing efficiency and a large proportion of empty capsids are major obstacles. This study focused on the Yin Yang 1 (YY1) binding motif (YY1-motif) and investigated the effect of its presence or insertion upstream of the Replicase (Rep)/Capsid (Cap) gene on AAV vector production. We found that the YY1-motif incidentally presented in a Rep/Cap plasmid was associated with high vector production. We then designed several modified Rep/Cap (RC2) constructs. The YY1-motif insertion in front of Rep/Cap gene increased vector yield in a repeat-number-dependent manner, and similar effects were not observed with other promoters insertion. Furthermore, the insertion of the YY1-motif reduced the amount of Cap protein per the same amount of full particle in supernatants on multiple serotypes, indicating the improvement in the empty/full capsid ratio. The YY1-motif insertion did not affect the AAV vector infectivity. These results denote that the YY1-motif has a universal regulatory function that optimizes the Rep/Cap expression balance, and simultaneously improves the production efficiency and full particle formation of AAV vectors. This finding could contribute to the development of highly efficient and high-quality AAV manufacturing processes.

microbiology↗

bioRxiv2023

Architecture of the Vertebrate Egg Coat and Structural Basis of the ZP2 Block to Polyspermy

Post-fertilization cleavage of glycoprotein ZP2, a major subunit of egg zona pellucida (ZP) filaments, is crucial for mammalian reproduction by irreversibly blocking polyspermy. ZP2 processing is thought to inactivate a sperm-binding activity located upstream of the proteins cleavage site; however, its molecular consequences and connection with ZP hardening are unknown. Here we report X-ray crystallographic, cryo-EM and biochemical studies showing that cleavage of ZP2 triggers its oligomerization. Deletion of the ZP-N1 domain that precedes the cleavage site of mouse ZP2 allows it to homodimerize even without processing, and animals homozygous for this variant are subfertile by having a semi-hardened ZP that allows sperm attachment but hinders penetration. Combined with the structure of a native egg coat filament, which reveals the molecular basis of heteromeric ZP subunit interaction, this suggests that oligomerization of cleaved ZP2 cross-links the ZP, rigidifying it and making it physically impenetrable to sperm.

biophysics↗

bioRxiv2022

Assembly of neuron- and radial glial cell-derived extracellular matrix molecules promotes radial migration of developing cortical neurons

Radial neuronal migration is a key neurodevelopmental event for proper cortical laminar organization. The multipolar-to-bipolar transition, a critical step in establishing neuronal polarity during radial migration, occurs in the subplate/intermediate zone (SP/IZ), a distinct region of the embryonic cerebral cortex. It has been known that the extracellular matrix (ECM) molecules are enriched in the SP/IZ. However, the molecular constitution and functions of the ECM formed in this region remain poorly understood. Here, we identified neurocan (NCAN) as a major chondroitin sulfate proteoglycan in the SP/IZ. NCAN binds to both radial glial cell-derived tenascin-C (TNC) and hyaluronan (HA), a large linear polysaccharide, forming a ternary complex of NCAN, TNC, and HA in the SP/IZ. Developing cortical neurons make contact with the ternary complex during migration. The enzymatic or genetic disruption of the ternary complex impairs radial migration by suppressing the multipolar-to-bipolar transition. Furthermore, both TNC and NCAN promoted the morphological maturation of cortical neurons in vitro. The present results provide evidence for the cooperative role of neuron- and radial glial cell-derived ECM molecules in cortical development.

neuroscience↗

bioRxiv2021

Archaeal origins of gamete fusion

Sexual reproduction consists of genome reduction by meiosis and subsequent gamete fusion. Presence of meiotic genes in prokaryotes suggests that DNA repair mechanisms evolved toward meiotic recombination; however, fusogenic proteins resembling those found in eukaryotes were not identified in prokaryotes. Here, we identify archaeal proteins that are homologs of fusexins, a superfamily of fusogens that mediate eukaryotic gamete and somatic cell fusion, as well as virus entry. The crystal structure of a trimeric archaeal Fusexin1 reveals novel features such as a six-helix bundle and an additional globular domain. Ectopically expressed Fusexin1 can fuse mammalian cells, and this process involves the additional domain and a conserved fusion loop. Archaeal fusexin genes exist within integrated mobile elements, potentially linking ancient archaeal gene exchanges and eukaryotic sex. One-Sentence SummaryCell membrane fusion proteins of viruses and eukaryotes are also present in archaea.

evolutionary biology↗

bioRxiv2021

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6x genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.

genomics↗

bioRxiv2019

Molecular basis of egg coat cross-linking sheds light on ZP1-associated female infertility

Interaction between sperm and the egg zona pellucida (ZP) is the first step of mammalian fertilization, and ZP component ZP1 is important for fertility by covalently cross-linking ZP filaments into a matrix. Like ZP4, a structurally-related subunit absent in the mouse, ZP1 is predicted to contain an N-terminal ZP-N domain of unknown function. Characterization of ZP1 proteins carrying mutations from infertile patients suggests that, unlike in the mouse, filament cross-linking by ZP1 is crucial for human ZP assembly. We map the function of ZP1 to its ZP-N1 domain and determine crystal structures of ZP-N1 homodimers from a chicken homolog of ZP1. These reveal that ZP filament cross-linking is highly plastic and can be modulated by ZP1 fucosylation and, potentially, zinc sparks. Moreover, we show that ZP4 ZP-N1 forms non-covalent homodimers in chicken but not human. Together, these data identify human ZP1 cross-links as a promising target for non-hormonal contraception.

biophysics↗