Biology subjects

Hayashi, M.

Publications and source records attributed to Hayashi, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Cholesterol constrains pore formation by mammalian gasdermins

Pyroptosis is a lytic form of cell death executed by gasdermin pores. Through a CRISPR screen to uncover macrophage genes required for gasdermin D (GSDMD) pore activity, we identify the endosome adaptor Rabgef1 as a positive regulator of pore formation. Rabgef1 deficiency preserves NT-GSDMD membrane binding but prevents NT-GSDMD oligomerization and lytic death. Mechanistic analyses revealed that Rabgef1 deficiency is associated with an overabundance of cholesterol in the plasma membrane. Cholesterol depletion or redistribution through multiple approaches restores GSDMD oligomerization and pyroptosis. The Rabgef1-mediated control of membrane cholesterol and pore formation was found to be a general regulator of the gasdermin family. In cancer cells, organoids, and tumors, cholesterol reduction sensitizes resistant cells to GSDME pyroptosis driven by synthetic mRNAs, chemogenetic induction, and chemotherapy treatment. These results establish membrane cholesterol content as an endogenous checkpoint for gasdermin-mediated pyroptotic cell death during the execution phase, with implications for metabolic disease and cancer immunotherapy.

immunology↗

bioRxiv2026

Engineered Chimeric Proteins Functionally Replace ALS-causing Endogenous FUS and TDP-43 to Improve Neuronal Health

Mislocalization and aggregation of the RNA-binding proteins (RBPs) FUS and TDP-43 are pathological hallmarks of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), contributing to combined loss- and gain-of-function toxicity. Here, we present a protein engineering strategy that appends optimized anti-aggregation motifs to FUS and TDP-43, thereby enhancing their nuclear localization and solubility, and enabling functional replacement of disease-associated proteins. We show that these engineered chimeric RBPs reduce levels of aggregation-prone endogenous proteins through autoregulatory mechanisms. In addition, chimeric FUS and TDP-43 recapitulate key nuclear functions, including DNA repair and mRNA processing. Notably, chimeric FUS restores neurite outgrowth in diseased iPSC-derived neurons, while chimeric TDP-43 suppresses cryptic exon inclusion in patient-derived fibroblasts. Collectively, these results demonstrate that engineered chimeric RBPs can rebalance RBP homeostasis by simultaneously addressing protein aggregation and mislocalization, thus mitigating RBP-associated loss- and gain-of-function toxicity, highlighting a generalizable strategy for therapeutic protein replacement in neurodegenerative disease.

neuroscience↗

bioRxiv2026

Osteocyte State Transitions Modulate Bone Remodeling During Early Skeletal Aging

Osteocytes are long-lived cells that play a central role in bone homeostasis, yet age-related changes in their functional states remain poorly understood, particularly because skeletal aging involves multiple processes beyond cellular senescence. We generated an osteocyte-specific MepeCre mouse line and combined osteocyte ablation in young and middle-aged mice with skeletal phenotyping, single-cell transcriptomics, and senolytic treatment. MepeCre-driven recombination was largely confined to osteocytes, with minimal off-target activity. Osteocyte ablation increased bone mass at both ages, indicating that osteocytes constrain bone accrual as part of their role in skeletal homeostasis. However, the accompanying remodeling changes differed with age: enhanced osteoblast activity predominated in young mice, whereas reduced osteoclast-mediated bone resorption predominated in middle-aged mice. Single-cell transcriptomics revealed distinct osteocyte subpopulations whose relative abundance shifted with age, from a predominantly matrix-enriched state in young mice to an expanded aging-transitional state in middle-aged mice. Although this state showed partial enrichment of senescence-associated transcriptional signatures, senolytic treatment failed to recapitulate the increase in bone mass induced by osteocyte ablation. Osteocyte therefore regulate bone mass through age-dependent mechanisms that coincide with shifts in osteocyte-state composition. These changes emerge by middle age and may contribute to early remodeling imbalance before overt cellular senescence during skeletal aging. Graphical AbstractGraphical summary of the findings of this study. AA, amino acids; NA, nucleic acid; UA, uric acid; TCA, tricarboxylic acid.

molecular biology↗

bioRxiv2026

Gingipain-containing products from Porphyromonas gingivalis promote epithelial CCL20 signaling and γδ T-cell accumulation in COPD-like airways

Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory airway disease in which impaired mucosal barrier function may increase susceptibility to aspirated oral microbial products. Periodontal disease has been associated with COPD development and exacerbation, but the epithelial mechanisms linking periodontal pathogens to pulmonary immune remodeling remain unclear. Here, we investigated whether gingipain-containing Porphyromonas gingivalis culture supernatant (PCS) promotes {gamma}{delta} T-cell-associated inflammation in COPD-like airways. Repeated intratracheal administration of PCS to {beta}ENaC-transgenic mice induced airway-centered immune cell accumulation and increased {gamma}{delta} TCR-positive cell accumulation, together with elevated expression of the {gamma}{delta} T-cell-associated cytokines Ifng and Il17a. PCS also increased pulmonary Ccl20 and Ccr6 expression, whereas epithelial alarmin-related genes and M2 macrophage-associated responses were not induced in parallel. In ENaC-overexpressing human airway epithelial cells, PCS induced CCL20 and F2RL1, the gene encoding protease-activated receptor 2 (PAR-2), and reduced the N-terminal PAR-2 signal, consistent with proteolytic receptor cleavage. Direct PAR-2 activation reproduced CCL20 induction, whereas pharmacological PAR-2 inhibition suppressed PCS-induced CCL20 expression. In contrast, PAR-1 inhibition or LPS neutralization with polymyxin B did not suppress this response. These findings support a mucosal epithelial protease-sensing model in which gingipain-containing P. gingivalis products activate PAR-2-dependent CCL20 production in airway epithelial cells and are associated with CCR6-linked {gamma}{delta} T-cell accumulation in COPD-like airways. Contribution to the field statementPeriodontal disease is often associated with chronic obstructive pulmonary disease, but how oral bacterial products affect lung inflammation remains unclear. This study shows that protease-rich products from the periodontal pathogen Porphyromonas gingivalis can be sensed by airway epithelial cells under COPD-like conditions. This response induces a chemokine signal that is linked to the accumulation of {gamma}{delta} T cells, a type of immune cell involved in inflammatory responses. Our findings suggest that the airway epithelium acts as an immune sensor, converting signals from aspirated oral bacterial protease into lung inflammation. This work provides a mechanistic framework for understanding how oral dysbiosis may contribute to immune remodeling in COPD.

immunology↗

bioRxiv2026

Stromal state plasticity defines risk and therapeutic opportunity in recalcitrant inflammatory bowel disease

Inflammatory bowel diseases (IBD) remain a relapsing, treatment-refractory disorder marked by progressive tissue injury and inflammation despite expanding immune-targeted therapies. We established a prospective cohort integrating stromal biobanking, functional phenotyping, cross-cohort benchmarking, and outcome modeling to define disease-anchored cellular states. Colonic myofibroblasts from 34 individuals spanning health, ulcerative colitis, and Crohns disease resolved into two dominant states: inflammatory (IMFs) and quiescent (QMFs) myofibroblasts. QMF predominance forecasted remission, whereas IMF predominance increased the odds of worsening endoscopic severity despite therapy escalation during follow-up by [~]4.6-fold, linking early stromal biology to clinical outcomes. Unlike QMFs, IMFs exhibited a senescence-associated secretory phenotype that impaired epithelial stemness, barrier integrity, and innate immune fitness. State-guided prioritization identified EDNRB-antagonism as a high-confidence stromal intervention, reversing pathogenic phenotypes across orthogonal assays and species. Outcome simulation positioned stromal-state reversibility by EDNRB-antagonism as a precision axis, reducing odds of recalcitrance by [~]96.4% and reframing treatment resistance as a reversible stromal state. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/720931v2_ufig1.gif" ALT="Figure 1"> View larger version (88K): org.highwire.dtl.DTLVardef@3b2c50org.highwire.dtl.DTLVardef@da5400org.highwire.dtl.DTLVardef@1c100c1org.highwire.dtl.DTLVardef@1882e1_HPS_FORMAT_FIGEXP M_FIG C_FIG In this work, Tindle et al. identify reversible stromal states that govern remission vs. recalcitrant outcomes in IBD and nominate precision reprogramming of pathogenic myofibroblasts as a new therapeutic strategy.

physiology↗

bioRxiv2026

Characterization and therapeutic suppression of KEAP1-NRF2-driven resistance to KRAS inhibitors in pancreatic and lung cancer

The recent approval of KRAS inhibitors supports the therapeutic value of targeting mutant KRAS cancers. However, clinical efficacy is hindered by both primary and treatment-associated acquired resistance. We applied a CRISPR-Cas9 loss-of-function screen and identified loss of KEAP1 as a resistance mechanism to the KRASG12D-selective inhibitor MRTX1133 and the RAS(ON) multi-selective inhibitor RMC-7977 in pancreatic cancer models. RNA-sequencing analyses revealed a KEAP1KO transcriptome that is distinct from the ERK-, MYC-, and YAP/TAZ-TEAD-dependent transcriptional programs that drive KRAS inhibitor resistance, demonstrating a distinct mechanism of resistance. We then established a PDAC KEAP1-deficient (PKD) gene signature that was enriched in patients and preclinical models insensitive to KRAS inhibitor treatment. Finally, we observed that KEAP1-deficient cells exhibited elevated glutamine metabolism, and combination treatment with the glutamine antagonist DRP-104 (sirpiglenastat) enhanced KRAS inhibitor suppression of pancreatic and lung tumors. SIGNIFICANCEKEAP1 loss is associated with reduced response to KRAS inhibitor therapy. We demonstrate that KEAP1 loss-associated resistance can be overcome by pharmacologic inhibition of the KEAP1 loss-induced glutamine dependency, establishing a combination to enhance RAS inhibitor clinical efficacy.

cancer biology↗

bioRxiv2026

Coordinated Membrane Deformation Driven by a Minimal Set of Spiroplasma MreB Isoforms

Spiroplasma are wall-less helical bacteria that swim by switching the handedness of their helices. In most bacteria, MreB, a bacterial actin, forms relatively static filaments beneath the membrane to organize cell wall synthesis. In contrast, Spiroplasma eriocheiris encodes five MreB isoforms (SpeMreBs), and swimming requires a pair of isoforms, SpeMreB5 together with SpeMreB4 (or the related isoform SpeMreB1) (1) Yet how these MreBs generate force and membrane deformation remains unclear. To examine the membrane-deforming activities of SpeMreBs, we demonstrated a simple reconstitution system using the non-motile synthetic bacterium JCVI-syn3B and purified SpeMreBs expressed in Escherichia coli. Lysates of syn3B expressing SpeMreB5 deformed liposomes in a concentration-dependent manner. In contrast, lysates co-expressing both SpeMreB5 and SpeMreB4 showed a plateau in the frequency of deformation, suggesting that SpeMreB4 suppresses membrane deformation driven by SpeMreB5. Deformed liposomes exhibited either fluctuating or stable behaviors. ATP depletion changed both the frequency and behavior of deformation, indicating that membrane remodeling depends on the nucleotide state of SpeMreBs. Reconstitution with purified SpeMreBs from E. coli confirmed that SpeMreB5 alone deforms membranes, whereas SpeMreB1, a member of the same class as SpeMreB4, suppresses deformation. These results suggest that membrane shape in Spiroplasma is dynamically regulated by antagonistic interactions among isoforms of SpeMreBs isoforms and their nucleotide-dependent assembly states.

synthetic biology↗

bioRxiv2026

Chlamylipo, a Chlamydomonas-in-liposome microswimmer: self-propelled swimming and associated lipid membrane flow

Developing active transport systems for microcargo delivery is challenging and requires overcoming the low Reynolds number constraints. We developed a bio-hybrid micro-swimmer, "chlamylipo" consisting of the green alga Chlamydomonas reinhardtii, encapsulated within a giant liposome. Although internal encapsulation offers cargo protection, it requires a mechanism to transmit the propulsion force across a closed membrane. We demonstrated that chlamylipo exhibited forward swimming and phototactic directional control. High-speed imaging of membrane shape and fluid flow revealed that the driving force originated from periodic membrane deformations and was accompanied by characteristic fluid dynamics. Flow analysis showed rapid oscillations at tens of hertz corresponding to flagellar beating, superimposed on slower axial migration at approximately 4 Hz associated with cell rotation. Corresponding flow signatures were also detected in the external fluid, indicating mechanical coupling across the lipid bilayer. Membrane domain tracking further showed that fluid motions inside and outside the membrane were coupled through viscous friction and membrane deformation, generating a characteristic four-vortex flow field consistent with a two-point force model. Together, these results suggest that membrane flow mainly reflects force transmission across the bilayer, whereas forward propulsion is primarily driven by periodic membrane deformation. This study elucidates the physical mechanism of force transmission in encapsulated swimmers, demonstrating that internal hydrodynamic power can effectively drive the motion of macroscopic containers. SignificanceThe development of autonomous micro-swimmers for targeted drug delivery is a major challenge in biophysics. We present "chlamylipo," a hybrid system in which a swimming alga is encapsulated inside a lipid vesicle. This study is significant because it demonstrates that an enclosed swimmer can propel a macroscopic container solely via hydrodynamic coupling across a closed membrane without direct external mechanical links. Furthermore, we achieved external directional control using phototaxis. This study provides physical insights into fluid-membrane interactions and proposes a novel strategy for designing light-guided active transport carriers.

biophysics↗

bioRxiv2026

Design and validation of a novel portable electrode holder for motor-related EEG measurement

ObjectiveA simplified headset to measure electroencephalography (EEG) from sensorimotor areas is necessary to monitor motor-related neural responses accurately in real-world environments. The aim of the present study was to design and validate a novel, easy-to-use, and reliable EEG electrode holder that enables positioning of the EEG electrodes directly over the sensorimotor cortex, while enabling flexibility in relation to varying head size. ApproachThe spatial distribution of motor-related EEG activity was estimated using a dataset of high-density EEG (HD-EEG) from 82 participants. International databases of head shape were analyzed to determine dimensional requirements for a headphone-shaped holder. The proposed headset was validated by comparing its recordings with those obtained with a commercially available HD-EEG (Experiment 1) and by computing the actual position and recorded EEG motor-related activity obtained using the proposed holder (Experiment 2). Main resultsThe estimated distance between the measurement electrode and the top of the head, used as a design requirement for the proposed headset, ranged from 56.2 to 80.0 mm. Experiment 1 showed that the center frequencies of alpha-band recorded by the proposed and by the HD-EEG headsets were highly correlated (r=0.97). Experiment 2 showed that, by using the proposed headset, the actual placement of electrodes was within 8 mm from the ideal positions. Moreover, the experiment showed consistent results in terms of task-, location-, and frequency-specific modulation of sensorimotor activities in the alpha-band. For example, significant contralateral motor-related event-related desynchronization in the alpha-band, and significant alpha-band power increase during the eyes closed condition, namely event-related synchronization. SignificanceThe proposed electrode holder is easy to use and adjustable to compensate for varying head size and it may enable reliable measurement of motor-related EEG. It could support practical application of motor-related EEG acquisition in real-world contexts in several applications including sports, rehabilitation, and artistic performance.

neuroscience↗

bioRxiv2026

Dietary lipids attenuate IGF-1-Akt and injure epithelial-endothelial injury program that accelerates obstructive lung disease

Background Altered lipid metabolism is increasingly implicated in chronic obstructive pulmonary disease (COPD), but it remains unclear how a pre-existing obstructive lung state modifies the response to systemic lipid excess. We investigated whether high-fat diet (HFD) amplifies COPD-relevant lung injury and examined epithelial and vascular programs associated with this response. Methods Male wild-type (WT) and beta-epithelial sodium channel-transgenic ({beta}ENaC-Tg) mice were fed control diet or HFD for 10-11 weeks. Lung structure and function, whole-lung transcriptomes, Akt-FOXO1 signaling, apoptosis-related responses, and pulmonary vascular profiles were assessed. Streptozotocin-induced insulin-deficient diabetes and pharmacological IGF-1 receptor inhibition were used as mechanistic comparators. Palmitate responses were examined in human bronchial epithelial cells, ENaC-hyperactive epithelial cells, and endothelial cells, including conditioned-medium transfer. HFD preconditioning was also evaluated in an elastase-induced emphysema model. Statistical analyses included unpaired two-tailed Student's t tests, one-way ANOVA with Tukey-Kramer or Dunnett multiple-comparison testing, Pearson correlation, and Benjamini-Hochberg correction for RNA-sequencing analyses. Results HFD produced similar increases in body weight, glycemia, and adiposity in WT and {beta}ENaC-Tg mice, while further increasing distal-airspace enlargement and reducing FEV0.1/FVC in {beta}ENaC-Tg mice. Lung transcriptomics revealed coordinated remodeling of lipid metabolic, PI3K-Akt, and vascular programs. HFD reduced Akt phosphorylation, increased FOXO1 and Fasl, and increased TUNEL-positive cells in epithelial regions. Palmitate attenuated IGF-1-induced Akt activation in bronchial epithelial cells, whereas IGF-1 receptor inhibition reproduced Akt suppression and apoptosis-related responses without fully reproducing the HFD phenotype. HFD preconditioning also increased elastase-induced airspace enlargement, accompanied by parallel upregulation of FOXO1 and TUNEL positivity. HFD reduced pulmonary CD34-positive vascular profiles, and palmitate activated endothelial cells directly and through conditioned media from ENaC-hyperactive epithelium. In men with airflow obstruction, hepatic steatosis coincided with lower percent-predicted FEV1. Conclusions Dietary lipid stress amplifies obstructive lung injury and engages complementary epithelial and vascular responses. Impaired epithelial IGF-1-Akt signaling and epithelial-endothelial crosstalk provide a mechanistic framework linking systemic metabolic stress to reduced resilience of the obstructive lung.

molecular biology↗

bioRxiv2025

EC-isHCR: a rapid method for in situ hybridization chain reaction in diverse animal samples

The in situ hybridization chain reaction (isHCR) visualizes RNA across multiple spatial scales, from organs to subcellular structures, in diverse samples. We previously proposed a rapid protocol, EC-isHCR, for Drosophila embryos and ovaries. Whether EC-isHCR retains the features of conventional isHCR, including wide-spatial-scale analyses in various samples, however, has remained unclear. Here, we show that EC-isHCR enables robust RNA detection in a broad range of samples, such as whole-mount fruit fly, parasitoid wasp, and aphid preparations; paraffin sections of trout; frozen mouse sections; and human cultured cells. Moreover, EC-isHCR enabled detection of subcellular RNA localization. EC-isHCR also visualized co-localization of RNA with phase-separated condensates in fruit fly embryos and detected the protrusion-enriched mRNA in HeLa cells. To broaden the applicability of EC-isHCR, we developed an automated probe design tool (https://github.com/ShuntaYorimoto/hcrkit). By combining this tool with EC-isHCR, we provide a fast and versatile framework to visualize mRNAs. This framework will help reduce the barrier to using fast isHCR and thereby facilitate research across diverse areas of the life sciences. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/696653v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1852584org.highwire.dtl.DTLVardef@621682org.highwire.dtl.DTLVardef@1b3bf5corg.highwire.dtl.DTLVardef@1d86841_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- EC-isHCR enables rapid acquisition of high-contrast images. - EC-isHCR preserves features of conventional isHCR, including versatile sample compatibility and high-resolution imaging. - An automated probe design tool was developed for EC-isHCR. - EC-isHCR/probe tool framework will help reduce the barrier to using fast isHCR.

bioengineering↗

bioRxiv2025

Testing methodological and population-specific influences on the detection of Zipf's law of brevity in chimpanzee gestures

Zipfs law of brevity is a widespread manifestation of information compression found across human languages and other communication systems. Chimpanzee gesture represents a rare absence of its expression in short-range communication. But, whether this absence reflects a feature of ape gesture production, or results from methodological obstacles or population differences is unclear. Selecting the appropriate unit of analysis is crucial for detecting linguistic patterns in any system. We assess gestural repertoires of three chimpanzee communities for Zipfs law, while discriminating and testing different levels of unit durations (segmentation) and how finely gestural units are split (granularity). We report the first repertoire-wide detection of Zipfs law in ape gesture in one chimpanzee community at a specific level of segmentation and granularity. We suggest that both methodological and socio-ecological factors can shape the detection and expression of Zipfs law, emphasizing the importance of species-relevant units and metrics for meaningful cross-species comparisons.

animal behavior and cognition↗

bioRxiv2025

RNA G-Quadruplexes Function as a Tunable Switch of FUS Phase Separation

FUS undergoes liquid-liquid phase separation (LLPS) to support essential cellular functions, but aberrant phase transitions promote toxic aggregation in neurodegenerative disease. Short RNA oligonucleotides can reverse this behavior, yet the structural determinants that govern RNA activity remain poorly defined. Here, we identify RNA G-quadruplexes (rG4s) as tunable structural motifs that potently modulate FUS LLPS. rG4 activity depends on its concentration and is modulated by rG4 length and stability: increasing repeat number switches rG4s from inhibitor to nucleator of FUS assembly, whereas chemical modifications that stabilize rG4 enhance inhibitory function and render these activities resilient to ionic perturbation. Although short rG4s interact with both soluble and condensed FUS, they preferentially engage the soluble pool, likely shifting the equilibrium toward dispersion. Leveraging these mechanistic insights, we developed a bioinformatic pipeline that uncovered more rG4 inhibitors that robustly reverse FUS LLPS and aggregation. Our findings establish rG4s as chemically programmable regulators of protein phase behavior and provide a blueprint for engineering RNA-based therapeutics that dissolve pathogenic FUS assemblies. More broadly, this work directly links RNA secondary structure to distinct functional outcomes in phase behavior, establishing a structure-function paradigm for RNA control of condensates, demonstrating implications in both fundamental biology and therapeutic development. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/685846v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1db3ea8org.highwire.dtl.DTLVardef@eec825org.highwire.dtl.DTLVardef@96187eorg.highwire.dtl.DTLVardef@2204ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis

BackgroundMany maternal mRNAs in Drosophila primordial germ cells (PGCs) are degraded in concert with the synthesis of new transcripts from the zygotic genome during gastrulation and germ band elongation. However, few studies have focused on maternal mRNA destabilization in PGCs at the blastoderm stage that is prior to zygotic genome activation (ZGA). Thus, the stability of maternal mRNAs at this stage and regulation of their degradation remain poorly understood. To address this gap, we examined the role of Nanos, an RNA-binding protein known to promote mRNA degradation, in blastoderm-stage PGCs. ResultsBy combining flow cytometry and RNA-seq analysis of PGCs, we identified the transcripts of 898 genes that were increased in nanos- PGCs. Among them, maternal mRNAs encoded by 298 genes were downregulated by Nanos in PGCs. ConclusionsOur results show that Nanos downregulates maternal mRNA expression in PGCs before ZGA. As Nanos in C. elegans PGCs has also been reported to promote maternal-to-zygotic transition (MZT) via maternal mRNA downregulation during a transcriptionally silent state, our findings highlight the importance of investigating the function of Nanos for understanding the MZT in PGCs across various animal species.

developmental biology↗

bioRxiv2025

Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut

Cellular plasticity, the ability of a differentiated cell to adopt another phenotypic identity, is restricted under basal conditions, but can be elicited upon damage to facilitate regeneration. Such damage-induced cellular plasticity restores homeostasis and prevents pathology, yet its underlying molecular basis remains largely unexplored. Here, we reported damage-induced cellular plasticity of secretory enteroendocrine cells (EEs) in the adult Drosophila midgut. We found that ionizing radiation enhanced EE plasticity such that it promoted EEs to dedifferentiate into ISCs and subsequently re-differentiate towards ECs. We identified that radiation induced the production of a stress-inducible transcription factor Xrp1 in EE lineages, and its upregulation was necessary for EE plasticity. Single-cell RNA sequencing of guts with EE-specific Xrp1 overexpression revealed ectopic expression of progenitor-specific genes in EEs, which was necessary for Xrp1 to drive EE plasticity. Our work provides a mechanistic framework for understanding cellular plasticity and suggests its potential role in damage-induced responses.

cell biology↗

bioRxiv2025

Rhizobial infection-specific accumulation ofphosphatidylinositol 4,5-bisphosphate inhibits the excessive infection of rhizobia in Lotus japonicus

O_LIDuring the symbiosis of legume with nitrogen-fixing bacteria, collectively called rhizobia, suppression of excessive rhizobial infection by host plants is important to maximize the benefits of symbiotic nitrogen fixation. However, it remains relatively poorly understood the molecular mechanism involved in the suppression. C_LIO_LIWe performed LC-MS and RNA-seq analysis using rhizobia-infected Lotus japonicus roots and investigated the role of phosphatidylinositol (PI) and phosphatidylinositol phosphates (PIPs) in the symbiosis. Phosphatidylinositol transfer protein (PITP)-like proteins 4 (PLP4), phosphatidylinositol 3-phosphate 5-kinase 4 (PIP5K4) and PIP5K6 mutants, which are involved in the vesicular transport of lipids and phosphorylation of PIPs, were used to show the involvement of the signaling of PI and PIPs. Accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] during rhizobial infection were examined by a fluorescent marker 1xTUBBY-C (TUBBY). C_LIO_LIWe found that PI signaling-related genes were upregulated, and the amount of PIP2 increased in L. japonicus roots during rhizobial infection. In the PLP4, PIP5K4 and PIP5K6 mutants, rhizobial infection increased and PIP2 accumulation was failed. Furthermore, the observation of PI(4,5)P2 in rhizobia-infected roots revealed that the ectopic accumulation was closely related to suppression of rhizobial infection. C_LIO_LIOur findings indicate that the accumulation of PI(4,5)P2, which is mediated by PLP and PIP5Ks, suppresses excessive rhizobial infection in the root epidermis and cortex, leading to the optimal number of nodules. C_LI

plant biology↗

bioRxiv2025

Somatic gene repression ensures physical segregation of germline and soma in Drosophila embryos

In many animals, primordial germ cells are transiently segregated outside the somatic-cell cluster that forms the embryos body during early embryogenesis. This physical segregation of germline from the soma has been long believed to be crucial for germline development, but the mechanisms controlling this segregation and its developmental significance remain unclear. Here, in Drosophila, we show that somatic gene silencing in the germline is essential for maintaining this segregation. We showed that primordial germ cells (pole cells) lacking the Nanos- and Polar granule component (Pgc)-dependent dual repression mechanism caused misexpression of widespread somatic genes. They formed abnormal cellular protrusions, invaded adjacent somatic epithelium, and intermingled with somatic cells. These mislocalized pole cells ultimately underwent cell death, whereas properly segregated cells survived. Notably, the knockdown of miranda (mira), one of the somatic genes expressed ectopically in the pole cells lacking this repression mechanism, rescued these phenotypes. Our findings provide the first evidence that somatic gene silencing in germline is essential for preserving the physical segregation between germline and soma, highlighting its role in ensuring germline viability during early development.

developmental biology↗

bioRxiv2025

Concerted genome expansion of heritable symbionts in an insect host

Maternally transmitted symbionts represent important components of arthropod biology, acting as both beneficial partners and as reproductive parasites. Their strict vertical transmission greatly reduces their effective population size, making selection less efficient and driving a pattern of molecular evolution where genome size reduces. Contrastingly, there are sporadic observations of genome expansion in symbionts from clades where the genome has previously reduced in size. It is currently unclear whether these events are an idiosyncratic consequence of exposure to novel active mobile elements, or are driven by the host context. In this paper, we report the concerted genome expansion of two co-infecting heritable symbionts that supports a host-related driver of expansion. We assembled the genomes of Spiroplasma and Rickettsia bacteria that co-infect the lacewing Mallada desjardinsi. Both symbionts had the largest genome reported to date in their clade, approximately twice the median size for their respective genus. Genome expansion was driven by proliferation of mobile elements in both cases, but the underpinning elements were distinct. The observation that the proximate causes of expansion differed between symbionts led us to reject the hypothesis that concerted expansion was driven by a common mobile element invasion. We hypothesize these processes are driven either by bottleneck events impacting host population size, by the host environment causing stress-induced activation of mobile genetic elements, or by both symbionts having undergone a recent and coincident transition to vertical transmission.

genomics↗