Biology subjects

Kinoshita, M.

Publications and source records attributed to Kinoshita, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Extraocular Photoreception Controls nocturnal hatching via a neuroendocrine pathway in False Clownfish

Hatching is the transition from embryo to larva in oviparous animals. Birds, reptiles, and insects rupture the eggshell mechanically, whereas fish and amphibians digest the egg envelope using hatching enzymes. When and where larvae emerge influences their fitness. Many species regulate hatching timing using environmental cues, such as light, oxygen availability, and physical stimuli. In fish, hatching is driven by a neuroendocrine event that triggers hatching enzyme secretion; however, the mechanisms controlling this event are unknown. Using the false clownfish Amphiprion ocellaris, which hatches synchronously within 1-2 h after sunset, we showed that the role of thyrotropin-releasing hormone (TRH) as a hatching hormone, previously established in zebrafish and medaka, extended to clownfish, where TRH activated Ca2+; signaling in hatching gland cells through its receptor trhra, reinforcing the TRH-Ca2+-hatching enzyme axis as a conserved core module of teleost hatching. In clownfish, this module was additionally placed under upstream control by extraocular photoreception because dark-induced hatching persisted in eyeless embryos. This photoreceptive system was most sensitive to green light (550 nm), and several opsins with absorbance maxima in the corresponding middle- to long-wavelength range were expressed outside the eyes of pre-hatching embryos. Coupling extraocular photoreception to a conserved neuroendocrine module placed a critical life-history transition under stringent photic control, releasing larvae only in complete darkness, an adaptation that may have underpinned the success of this lineage in predator-rich coral reefs.

zoology↗

bioRxiv2026

Structural characterization of a pseudaminic acid-modified lateral flagellar filament from Vibrio alginolyticus

Bacterial flagellar filaments are often modified by glycans, but the structural basis and physiological significance of flagellin glycosylation remain poorly understood in many species. Vibrio alginolyticus produces lateral flagella for surface-associated motility in viscous environments, with LafA forming its filament as flagellin. A maf homolog encoding a putative flagellin glycosylation factor is located immediately downstream of lafA, suggesting that the lateral filament is glycosylated. To investigate this possibility, we purified the lateral flagellar filament from V. alginolyticus and determined the structure at 2.37 [A] resolution by electron cryomicroscopy. Upon model building of LafA in the map, we identified additional densities connected to five serine residues, possibly corresponding to O-linked pseudaminic acid modifications. Mass spectrometric analyses identified these modifications as pseudaminic acid attached to Ser148, Ser173, Ser183, Ser189, and Ser197. Deletion of maf abolished lateral flagella formation and motility, and these defects were restored by complementation with maf. These results demonstrate that the Vibrio lateral flagellar filament is extensively modified by pseudaminic acid and that Maf is required for filament formation. Our findings provide the first structural insight into the glycosylation of Vibrio lateral flagellar filament and establish a framework for understanding the role of flagellin glycosylation in surface-associated motility.

microbiology↗

bioRxiv2026

Chemical Boosting of Foldase Condensates Accelerates Oxidative Protein Folding

Dynamic biomolecular condensates play crucial roles in intracellular compartmentalization and physiological functions. While engineering tools for compartmentalization have expanded add-on functionalities, directly amplifying the inherent catalytic machinery within biological phase-separated droplets has remained elusive. Herein, we developed a phase-separated oxidative folding reaction chamber based on protein disulfide isomerase A6 (PDIA6) by chemically targeting its active site CxxC motif to enhance enzymatic activity within PDIA6 droplets. A para-substituted N-methylated pyridinylmethanethiol (pMePySH) enhanced the catalytic oxidative folding of bovine pancreatic trypsin inhibitor, proinsulin, and antibody up to 12-fold within in vitro PDIA6 droplets. Furthermore, pMePySH targeted PDIA6 foci within the endoplasmic reticulum, significantly promoting insulin secretion. These findings offer a powerful platform for the spatiotemporal manipulation of protein folding, with profound implications for the scalable manufacturing of therapeutic antibodies and other complex biopharmaceuticals.

bioengineering↗

bioRxiv2026

Structure of an active FlhA ring reveals allosteric coupling between substrate specificity and export engine activation

The bacterial flagellar type III secretion system transports structural subunits in a defined order to assemble the flagellum. FlhA is the core component of this nanomachine; its transmembrane domain functions as an ion-driven export engine and its cytoplasmic domain connected by a flexible linker forms a nonameric ring that controls substrate selection. The coupling mechanism of these activities has remained unclear because the transmembrane domain has resisted structural analysis. Here we identify linker deletions that autonomously activate the export gate and capture a functionally active, hook-type protein export state of the entire ring complex. Using cryo-electron microscopy, we determine the structure of the FlhA({Delta}331-347) ring at 2.73 [A] resolution. The structure shows linker-mediated docking of the cytoplasmic ring to the transmembrane ring to stabilize the entire ring while sterically excluding filament-type substrate binding. These findings reveal how the FlhA ring allosterically couples substrate specificity to ion-driven export during flagellar assembly.

microbiology↗

bioRxiv2026

A single conserved residue in FlhA couples export gate activation to substrate specificity switching

FlhA is a core component of the bacterial flagellar type III secretion system that functions as both an export engine and a switch regulator of substrate specificity. How these two processes are mechanistically coupled remains unclear. Here we identify a single conserved residue in FlhA, Arg-391, as a key molecular node that links export gate activation to substrate specificity switching. The R391A substitution blocks the transition from hook-type to filament-type secretion, resulting in polyhooks lacking filaments. An intermolecular salt-bridge formation of Arg-391 with Glu-351 of an adjacent FlhA subunit stabilizes the filament-type FlhA ring. Suppressor mutations in FlhA and the ruler protein FliK restore this interaction, indicating that FliK promotes the intermolecular salt-bridge formation during export switching. Moreover, Arg-391 is required for efficient ATPase-independent activation of the export gate. Together, these findings reveal an electrostatic mechanism by which FlhA coordinates export gate activation and substrate specificity switching during flagellar assembly.

microbiology↗

bioRxiv2026

De novo design of a peptide ligand for specific affinity purification of human complement C1q

Affinity purification is a essential technique for isolating highly purified proteins; however, generating affinity ligands require significant time and financial investment. To address these limitations, this study proposes a novel affinity chromatography method utilizing in silico-designed cyclic peptides as ligands. Targeting Complement C1q (C1q), a plasma protein that plays crucial roles in classical complement pathway, we employed the biomolecular structure prediction model, AlphaFold2, to design specific binding cyclic peptides. Based on these designs, we synthesized lariat-type cyclic peptides characterized by disulfide cyclization and biotinylation, which were subsequently immobilized on streptavidin carriers. Performance tests confirmed that the resulting column specifically captured C1q, allowing for elution via a standard NaCl concentration gradient. Notably, high selectivity was preserved even in the presence of plasma, underscoring the ligands practical robustness. By overcoming traditional constraints through (1) rapid and simple design, (2) high specificity, and (3) universal versatility without genetic modification, this de novo design strategy represents a potential breakthrough in protein purification technologies. HighlightsO_LIAI-driven de novo design generated a specific cyclic peptide ligand for Complement C1q C_LIO_LIThe synthetic ligand enabled one-step purification of Complement C1q directly from human plasma C_LIO_LIMild elution conditions preserved the targets oligomeric structure and native interactome C_LIO_LIThis label-free strategy offers a rapid, low-cost alternative to antibody-based chromatography C_LI

bioinformatics↗

bioRxiv2026

Cyclic peptides space: The methodology of sequence selection to cover the comprehensive physical properties

Cyclic peptides have emerged as a pivotal modality for next-generation therapeutics, due to their superior biocompatibility, high selectivity, and structural stability. While AI-driven peptide design has advanced rapidly, conventional optimization algorithms are often constrained by initialization biases, which impede the efficient exploration of the vast chemical space. Here, we propose a novel methodology that integrates the protein language model ESM-2 with cyclic permutation averaging of embeddings to resolve this bottleneck. This approach establishes a comprehensive "peptide space", a high-dimensional vector representation that encapsulates the physicochemical and structural attributes of cyclic peptides. Our analysis reveals that random sequence selection results in a heterogeneous distribution within this space, potentially underrepresenting specific functional regions. Conversely, navigating this defined peptide space enables the selection of libraries that uniformly span diverse molecular properties. In a proof-of-concept study designing binders for {beta}2-microglobulin ({beta}2m), we demonstrate that initial sequences uniformly sampled from our peptide space yield superior candidates more efficiently than those derived from random selection. Furthermore, this framework facilitates the quantitative assessment of mutational perturbations on global peptide properties, supporting rational decision-making for both broad exploration and local optimization. This "peptide space" concept provides a foundational framework for defining appropriate search boundaries and enhancing computational efficiency in AI-mediated drug discovery. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/710724v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1dd903eorg.highwire.dtl.DTLVardef@128f941org.highwire.dtl.DTLVardef@1041e13org.highwire.dtl.DTLVardef@1527b25_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Active removal of inhibitory components drives the flagellarType III Secretion Specificity Switch

Type III secretion (T3S) systems assemble bacterial nanomachines, including the flagellum and virulence-associated injectisomes, by exporting distinct classes of substrates in a defined temporal order. In both systems, completion of an early assembly intermediate triggers an irreversible switch from early to late substrate secretion. In the flagellar system, this switch is controlled by the secreted molecular ruler FliK acting on the core T3S component FlhB, but the molecular mechanism governing this transition has remained unclear. Here we show that removal of two components, Fluke and the cleaved C-terminal domain of FlhB (FlhBCCD), locks the secretion apparatus in a constitutive late secretion state. In these mutants, secretion specificity no longer requires completion of the hook-basal body or the FliK ruler, indicating that Fluke and FlhBCCD function to maintain the apparatus in early secretion mode. Consistent with this model, synchronized flagellar gene expression experiments reveal that FlhBCCD is retained during early assembly and is lost coincident with hook-basal body completion and activation of {sigma}28-dependent late gene expression of flagellin and chemosensory genes. Structural modeling of the FliK C-terminal switch domain and FlhBCCD supports a mechanism in which secretion of FliK promotes destabilization and ejection of FlhBCCD from the secretion apparatus. Disruption of a folded region within FliK switch domain uncouples secretion from switching, indicating that the timing of FliK unfolding during secretion is critical for activation of the specificity switch. These findings show that secretion specificity switching is driven by FliK-dependent removal of inhibitory components, rather than passive sensing of assembly completion. Significance StatementType III secretion (T3S) systems build complex bacterial nanomachines, including the flagellum and virulence-associated injectisomes, by exporting distinct classes of substrates in a defined temporal order. How these systems switch secretion specificity during assembly has remained a long-standing question. We demonstrate that the flagellar T3S specificity switch requires removal of two inhibitory components that actively maintain the apparatus in an early secretion state. Their FliK-dependent ejection irreversibly triggers the transition to late substrate export, revealing that secretion switching is controlled by active inhibitory regulation rather than passive sensing of assembly completion. These results define a molecular mechanism for hierarchical control in bacterial secretion systems and provide insights likely relevant to other T3S nanomachines.

microbiology↗

bioRxiv2026

Longitudinal in vivo human wound healing model defines key role for smooth muscle cells in ECM remodeling

BackgroundEffective skin wound healing is essential for restoring tissue integrity following injury. Repair proceeds through phases of hemostasis, inflammation, proliferation, and remodeling, but molecular mechanisms governing these stages remain poorly defined. Vascular niche cells (VNCs)-including endothelial cells, vascular smooth muscle cells (SMCs), and fibroblasts-are central regulators of healing, but the lack of longitudinal in vivo human data has limited identification of VNC-derived signals that distinguish effective repair from pathological healing such as ulcers. Thus, defining the regulation of VNCs in wound healing addresses a critical knowledge gap. MethodsWe developed a protocol for wound healing using dermal forearm punch biopsies to track longitudinal repair in healthy volunteers. Single-cell and spatial transcriptomics were performed to identify and validate signaling activities within VNCs. ResultsWe spatiotemporally defined the inflammation, proliferation, and remodeling phases of human skin wound healing with a focus on VNCs. Spatial analysis localized this activity for VNCs and immune cells within a heterogenous granulation zone that later led to re-epithelializion. Angiogenesis was dominated by Vegf, Egf and Hif1 signaling. Extracellular matrix (ECM) remodeling occurred through Collagen, Laminin, Thrombospondin, and Fibronectin. SMCs emerged as dominant drivers of injury-induced remodeling including basement membrane and interstitial ECM components compared to fibroblasts. This SMC-led program was further defined by robust induction of TIMP1, an inhibitor of matrix degradation, which localized to granulation tissue and correlated with re-epithelialization and wound resolution. Lastly, we compared remodeling factors between healing and non-healing human diabetic foot ulcers (DFUs). SMCs in non-healing DFUs had deficient expression for core remodeling factors, including TIMP1, indicating SMC activity is needed for effective healing. ConclusionWe identified an SMC-driven model of wound repair in which TIMP1-dependent activity underpins granulation zone formation. Failure of this program defined a mechanistic basis for impaired healing in ulcers, identifying SMCs and TIMP1 as therapeutic targets.

molecular biology↗

bioRxiv2025

Microglia-dependent LPS preconditioning prevents neuroinflammation-induced behavioral deficits in male mice

Neuroinflammation contributes to psychiatric disorders, but preventive strategies targeting brain immune cells remain unexplored. Here we demonstrate that low-dose lipopolysaccharide (LPS) preconditioning prevents systemic inflammation-induced behavioral abnormalities through microglia-dependent mechanisms in male mice. Mice received preconditioning with 0.2 mg/kg LPS or saline for two consecutive days, followed by high-dose LPS challenge (5 mg/kg) or saline seven days later. Behavioral assessment revealed that preconditioning specifically prevented social preference deficits induced by systemic inflammation (preference score: -0.49{+/-}0.19 vs 0.14{+/-}0.10, p<0.01), while showing limited effects on locomotor activity and depression-like behaviors. Additionally, LPS preconditioning prevented anxiety-like behavior in a chronic corticosterone model and attenuated hippocampal inflammatory gene expression. Immunohistochemical analysis demonstrated that preconditioning suppressed microglial activation in hippocampal CA1 region, particularly reducing PBR/IBA1 ratio (37.5{+/-}2.4% vs 27.6{+/-}2.8%, p<0.01), with less pronounced effects in CA3. Critically, pharmacological microglial depletion using PLX3397 during the preconditioning period completely abolished these protective effects, establishing the causal role of microglia. Flow cytometric analysis revealed preconditioning-induced shifts in brain macrophage subpopulations defined by TMEM119 and CD45 expression patterns. Transcriptomic profiling identified subpopulation-specific responses, with one subset showing LPS-response pathway enrichment despite minimal gene expression changes, while another displayed extensive but functionally non-specific transcriptional alterations. These findings establish microglial preconditioning as a novel preventive strategy for neuroinflammation-induced social behavioral deficits and suggest potential therapeutic applications for psychiatric disorders involving neuroinflammatory components.

neuroscience↗

bioRxiv2025

Cell-cell communication as underlying principle governing color pattern formation in fishes

The diverse pigmentation patterns of animals are crucial for predation avoidance and behavioral display, yet mechanisms underlying this diversity remain poorly understood. In zebrafish, Turing models have been proposed to explain stripe patterns, but it is unclear if they apply to other fishes. In anemonefish (Amphiprion ocellaris), we identified gja5b, a gene orthologous to zebrafish leopard and encoding a connexin involved in pigment cell communication, as responsible for the Snowflake phenotype. Using CRISPR/Cas9 and transgenesis, we recapitulate the Snowflake phenotype and show expression of gja5b in iridophores. A matching allele was recovered in zebrafish, revealing complementary requirements in both species. Our findings highlight conserved roles of gap junction mediated communication in pigment patterning across divergent teleosts.

developmental biology↗

bioRxiv2025

Fc-Free Single Chain Antibody mRNA Therapy for Airway Infection of Multidrug-Resistant Pseudomonas Aeruginosa

With the growing threat of antimicrobial resistance (AMR), alternatives to antibiotics are urgently needed. In this study, we developed mRNA-based therapeutics encoding single-chain variable fragment (scFv) antibodies that target the type III secretion system of Pseudomonas aeruginosa, a key AMR pathogen. Delivered intravenously via lipid nanoparticles, the scFv mRNA effectively protected mice from airway infections by mitigating lung inflammation, reducing bacterial load, and improving survival. Notably, this approach proved effective in clinically relevant models involving immunocompromised mice infected with multidrug-resistant, exoU-positive (highly cytotoxic) clinical isolates. The study also explores the potential of Fc-free scFv formulations, leveraging mRNA technology to overcome their short half-life through sustained protein production. Importantly, Fc-free scFv antibodies migrated more efficiently from the bloodstream to the airway epithelium--the primary site of infection--than their Fc-conjugated counterparts, resulting in efficient therapeutic outcomes. Overall, mRNA-encoded Fc-free scFv antibodies represent a promising strategy for combating AMR infections.

immunology↗

bioRxiv2025

Structural basis of flagellar rod assembly on the FliPQR protein-export channel

The FliPQR complex constitutes a channel for export of the bacterial flagellar proteins involved in axial structure assembly. It also serves as a template for flagellar rod assembly. A periplasmic gate, formed by the N-terminal -helices of FliP and FliR, remains closed until FliE assembles onto FliP and FliR. The mechanism by which FliE opens the gate and assembles has remained unclear. Here, we present a cryoEM structure of the FliPQR complex in closed form at 3.0 [A] resolution. A {beta}-cap formed by the N-terminal {beta}-strands of FliP and FliR creates a tight seal in the closed gate. Interaction of FliE with FliP and FliR induces a conformational change in FliP and FliR, with their N-terminal -helices move up and outward. Consequently, the N-terminal {beta}-strands of FliP and FliR start opening the periplasmic gate one after another and form a docking site for FliE to initiate rod assembly.

microbiology↗

bioRxiv2025

Pediococcus pentosaceus decreases α-synuclein accumulation and alleviates parkinsonism in Caenorhabditis elegans and Oryzias latipes

In Parkinsons disease (PD), -synuclein (Syn) accumulation drives neuropathological progression, establishing it as a potential therapeutic target. Lactic acid bacteria (LAB) provide various health benefits to the host and are expected to offer protective effects on neurological functions through the brain-gut connection, as indicated by animal studies. However, the protective effects of LAB against Syn are not well understood. We investigated whether LAB feeding could reduce Syn accumulation and improve mobility in transgenic Caenorhabditis elegans, an invertebrate model organism that expresses human Syn in muscle. Among the nine screened strains, Pediococcus pentosaceus suppressed Syn accumulation and the decrease in bending counts, a locomotion index in nematodes. Additionally, feeding P. pentosaceus to Oryzias latipes (medaka), a vertebrate model organism, alleviated PD-like behavioral defects induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. P. pentosaseus acts as a probiotic against PD, and PD model worms and medaka can be used to screen effective LAB for prevention.

microbiology↗

bioRxiv2024

STAT3 signalling enhances tissue expansion during postimplantation mouse development

STAT3 signalling has been studied extensively in the context of self-renewal and differentiation of mouse embryonic stem cells. Zygotic STAT3 is required for normal postimplantation development. On an outbred genetic background, Stat3 null embryos consistently lagged behind their littermates, beginning with significant reduction of epiblast cells at implantation. Remarkably, mutants closely resemble non-affected embryos from the previous day at all postimplantation stages examined. We pinpoint this phenotype to loss of the serine-phosphorylated form of STAT3 which predominates in postimplantation embryonic tissues. Bulk RNA-sequencing analysis of isolated mouse epiblasts confirmed Stat3 null embryos exhibited developmental delay transcriptionally. Single cell RNA sequencing of mid gestation chimaeras containing STAT3 null embryonic stem cells revealed exclusion of mutant cells exclusively from the erythroid lineage. Although Stat3 null embryonic stem cells can differentiate into erythroid and hematopoietic lineages in vitro, they are out-competed when mixed with wild type cells. Combined with the reduced size of STAT3 null epiblasts after implantation, our results implicate a role for STAT3 in cell proliferation affecting temporal control of embryonic progression and rapid differentiation. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.

developmental biology↗

bioRxiv2024

Structural insights into the assembly mechanism of the flagellar MS-ring with three different symmetries

The flagellar basal body MS-ring, formed by 34 FliF subunits, is the core of the flagellar motor as well as the base for flagellar assembly. The MS-ring is also a housing for the flagellar protein export gate complex that is required for construction of the flagellum on the cell surface. A large periplasmic region of FliF contains three ring-building motifs named RBM1, RBM2, and RBM3. RBM3 forms the S-ring and {beta}-collar with C34 symmetry. RBM2 forms the inner core ring of the M-ring with C23 symmetry surrounded by 11 cog-like structures formed by RBM1 and RBM2. However, it remains unknown how FliF assembles to generate these three different symmetries within the MS-ring. Here, we report the two cryoEM structures of the MS-ring formed by FliF co-expressed with FliG and transmembrane export gate proteins. Structural comparison of 33-mer and 34-mer MS-rings revealed that a subtle change in the conformation of RBM3 produces the different rotational symmetries. Combination of cryoEM structural and mutational analyses of the MS-ring with C33 symmetry provides evidence that the well-conserved DQxGxxL motif within a flexible loop connecting RBM2 and RBM3 allows RBM2 to take two different orientations relative to RBM3 to form not only 11 cog-like structures just outside the inner core ring with C22 symmetry but also an appropriately sized central pore in the inner core ring to accommodate the export gate complex. IMPORTANCEThe flagellar MS-ring is the core of the flagellar motor and serves not only as an initial template for flagellar assembly but also as a base to accommodate the flagellar protein export complex. The MS-ring is formed by 34 subunits of FliF with two transmembrane helices and a large periplasmic region containing ring-building motifs, RBM1, RBM2, and RBM3. FliF adopts two different conformations in the MS-ring to generate three different rotational symmetries, C34, C23, and C11. However, how FliF assembles to produce these three symmetries remains a mystery. Combination of cryoEM structural and mutational analyses has provided evidence that the well-conserved DQxGxxL motif within a hinge loop connecting RBM2 and RBM3 allows RBM2 to take two different orientations relative to RBM3, allowing 23 RBM2 domains of 34 subunits to form the inner core ring with a properly sized central pore to accommodate the flagellar protein export complex.

microbiology↗

bioRxiv2024

Structural analysis of S-ring composed of FliFG fusion proteins in marine Vibrio polar flagellar motors

The marine bacterium Vibrio alginolyticus possesses a polar flagellum driven by a sodium ion flow. The main components of the flagellar motor are the stator and rotor. The C-ring and MS-ring which are composed of FliG and FliF, respectively, are parts of the rotor. Here, we purified an MS-ring composed of FliF-FliG fusion proteins and solved the near-atomic resolution structure of the S-ring--the upper part of the MS-ring--using cryo-electron microscopy. This is the first report of an S-ring structure from Vibrio whereas, previously, only those from Salmonella have been reported. The Vibrio S-ring structure reveals novel features compared to that of Salmonella such as tilt angle differences of the core domain and the {beta}-collar region, the decrease of the inter-subunit interaction between core domains, and altered electrostatic inner-surface. The residues potentially interact with other flagellar components, such as FliE and FlgB, are well structurally conserved in Vibrio S-ring. These comparisons clarified the conserved and non-conserved structural features of the MS-ring across different species. IMPORTANCEUnderstanding the structure and function of the flagellar motor in bacterial species is essential for uncovering the mechanisms underlying bacterial motility and pathogenesis. Our study revealed the structure of the Vibrio S-ring, a part of its polar flagellar motor, and highlighted its unique features compared with the well-studied Salmonella S-ring. The observed differences in the inter-subunit interactions and in the tilt angles between the Vibrio and Salmonella S-rings highlighted the species-specific variations in the flagellar assembly. By concentrating on the region where the S-ring and the rod proteins interact, we uncovered conserved residues essential for the interaction. Our research contributes to advancing of bacterial flagellar biology.

biophysics↗

bioRxiv2024

Effect of Light and Water Agitation on Hatching Processes in Clown Anemonefish Amphiprion ocellaris

Clown anemonefish (Amphiprion ocellaris) exhibit an environmentally cued hatching strategy, wherein parents generate water flow to encourage embryos to hatch after sunset on the eighth day post spawning. Although previous studies have shown that hatching requires complete darkness and water agitation, the regulatory mechanisms underlying these environmental cues remain elusive. This study investigated the expression patterns of hatching enzymes and how darkness and water agitation affect their secretion and the digestion of the egg envelope (chorion) in clown anemonefish. We revealed that hatching enzymes were expressed from the early developmental stages and decreased towards hatching day, similar to other fish species. The hatching gland cells were located on the tail, which may be associated with egg shape and chorion breakage. On the day of hatching, chorion digestion occurred exclusively in complete darkness, regardless of water agitation. In addition, ionomycin, a Ca2+ ionophore and an inducer of hatching enzyme secretion, triggered chorion digestion even under light-on conditions. Furthermore, water agitation expedited chorion digestion in the dark. In conclusion, our findings indicate that darkness triggers the secretion of hatching enzymes mediated by changes in Ca2+ levels, whereas water agitation assists chorion digestion activity and/or hatching enzyme secretion. These responses to environmental cues contribute to the rapid and synchronised hatching in clown anemonefish. Summary statementLight conditions and water agitation regulate the secretion of hatching enzymes and the chorion digestion activity, thereby facilitating a rapid hatching response to environmental changes in clown anemonefish.

physiology↗