Biology subjects

Chen, Q.

Publications and source records attributed to Chen, Q..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Salmonella exploits metal-responsive UMPylation to enable intracellular biphasic growth and antibiotic tolerance

Salmonella develops profound antibiotic tolerance during in vivo infection, directly contributing to antimicrobial treatment failure. Although phenotypic heterogeneity in bacterial growth rates underlies this tolerance, the exact mechanisms remain elusive. Here, we reveal that Salmonella exhibits a biphasic growth pattern within macrophages, with initial antibiotic levels modulating lag phase duration. Crucially, this growth plasticity is orchestrated by metal ion homeostasis and a reversible PTM-mediated protein phase transitions. Mechanistically, under stress conditions, enhanced Mn2+ uptake activates the UMPylator YdiU, which modifies critical translational machinery components such as elongation factor TufA. These modifications induce protein aggregation, leading to translational arrest and growth stasis. Conversely, upon stress alleviation, Salmonella accumulates Mg2+ and effluxes Mn2+, then the de-UMPylase YdiV is activated, which resolves protein aggregates to enable rapid bacterial resuscitation and proliferation. This metal-responsive proteostatic switch represents an evolutionarily conserved strategy for bacterial stress adaptation, with broad implications for combating antimicrobial tolerance. SIGNIFICANCE STATEMENTAntibiotic tolerance, a key cause of treatment failure in chronic infections, is often linked to bacterial phenotypic heterogeneity, yet the underlying regulatory mechanisms remain largely understood. This study uncovers a fundamental survival strategy employed by intracellular pathogen Salmonella, where host-derived manganese acts as a critical signal to induce a reversible, dormant state. We demonstrate that stress-induced Mn2+ influx activates widespread protein UMPylation, which functions as a molecular glue to drive the aggregation of essential proteins, thereby halting bacterial growth and conferring antibiotic tolerance. Crucially, this state is reversible upon stress relief through Mn2+ efflux and subsequent de-UMPylation, enabling rapid bacterial resuscitation. As an evolutionarily conserved mechanism of adaptive tolerance, this metal-ion-responsive switch, mediated by reversible protein UMPylation, identifies a key target for developing therapeutics against persistent bacterial infections.

microbiology↗

bioRxiv2026

Intra-annual precipitation variability mutes or magnifies the impact of wet and dry years on plant biomass.

As the atmosphere warms, both the amount and timing of precipitation are changing, but how those two trends interact to influence plant growth remains unresolved. Using 5-15 years of data from 48 globally distributed grassland sites, we quantified how the temporal distribution of precipitation within the year (evenness) interacts with annual precipitation amount and nutrient limitation to influence plant biomass. Annual precipitation anomalies had a large influence on plant biomass when intra-annual precipitation was more evenly distributed (frequent small events) and little impact when less even (infrequent large events). This relationship was consistent across aridity gradients and nutrient limitations and strongest in systems with warm wet seasons. Our work shows that the response of plant systems to changes in annual precipitation amount are largely dependent on how evenly it is temporally distributed.

ecology↗

bioRxiv2026

SWI/SNF nuclear foci scaffold peripheral gene hubs for circadian chromatin control

How dynamic circadian rhythms arise from a relatively static nuclear architecture remains a fundamental open question. Here, we identify the SWI/SNF chromatin-remodeling complex as a critical interface between the circadian clock and nuclear organization. Using endogenously tagged Moira (MOR), a core component of the Drosophila SWI/SNF complex and homolog of human BAF155, we find that MOR assembles into a small number of discrete foci near the nuclear periphery, in stark contrast to the current model of diffuse nuclear distribution for SWI/SNF-family proteins. We demonstrate that this localization is maintained by the inner nuclear envelope LEM-domain protein Otefin, effectively shifting MOR from a global to a localized regulator of chromatin architecture. DNA-FISH reveals that clock-regulated genes cluster into peripheral "hubs" that co-localize with MOR foci throughout the circadian cycle. ATAC-seq analysis shows that while MOR modulates chromatin accessibility genome-wide, it establishes a constitutive restrictive baseline specifically at clock-regulated loci. As a result, MOR depletion abolishes accessibility rhythms at these loci, rendering them constitutively hyper-accessible. This deregulation disrupts rhythmic gene expression and ultimately drives behavioral arrhythmia. Strikingly, oscillations of the core clock proteins PER and TIM remain intact, indicating that MOR loss uncouples the protein oscillator from its genomic output. Together, these results reveal that MOR-containing SWI/SNF foci form a stable perinuclear scaffold that gates chromatin accessibility, enabling the core clock machinery to convert transient protein oscillations into high-amplitude transcriptional rhythms. Significance StatementHow dynamic circadian rhythms emerge from a relatively static nuclear architecture remains a fundamental mystery. Here, we challenge the assumption that clock-target genes are randomly distributed by identifying a precise nuclear organization where these genes cluster into peripheral hubs. These hubs co-localize with stable SWI/SNF (MOR) foci anchored at the nuclear envelope. We demonstrate that this perinuclear scaffold is essential for gating rhythmic chromatin accessibility. Most importantly, loss of this architecture uncouples robustly oscillating clock protein program from its genomic and behavioral outputs. These findings reveal that circadian timekeeping is not merely a biochemical process but a spatially organized one, where nuclear topology licenses the translation of time into circadian rhythms.

cell biology↗

bioRxiv2026

ChromBERT-tools: A versatile toolkit for context-specific embedding of transcription regulators across different cell types

MotivationRepresentations that capture the genome-wide context of transcription regulators are critical for establishing a shared backbone for flexible transcription modeling and in silico regulatory analysis. Yet, current embeddings predominantly rely on limited modalities, such as gene co-expression or static protein features, offering an incomplete perspective that ignores context-dependent transcription regulator activities across the genome. The lack of transcription regulation-informed embeddings, paired with the absence of a user-friendly and lightweight toolkit for their generation, adaption to different cell types and interpretation, impedes the capture of the regulatory logic that underpin cellular states and functions. ResultsTo address this need, we present ChromBERT-tools, a lightweight toolkit designed to operationalize regulation-informed embeddings derived from a foundation model pre-trained on the comprehensive landscapes of human and mouse transcription regulators. ChromBERT-tools provides user-friendly command-line interfaces (CLIs) and Python APIs to achieve two primary goals: (i) generating cell-type-agnostic embeddings that capture the semantic representations of individual regulators and their combinatorial interactions, serving as biological priors of transcription regulator modality to enhance transcription regulation modeling and rule interpretation; and (ii) generating cell-type-specific embeddings via fine-tuned model variants, which support in silico inference of regulatory roles of transcription regulators in cell types with scarce experimental data. The toolkit streamlines end-to-end workflows for embedding generation, adaption to different cell types and interpretation towards biological inferences such as regulator-regulator interaction across the genome and key regulators determining cell identity or cell state transition. Availability and implementationChromBERT-tools is freely available at https://github.com/TongjiZhanglab/ChromBERT-tools, with documentation at https://chrombert-tools.readthedocs.io/en/latest/.

bioinformatics↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Mechanism study on lactic acid promoting intervertebral disc degeneration by regulating senescence and DNA damage of cartilage endplate stem cells

Intervertebral disc degeneration, a leading cause of low back pain with incompletely elucidated molecular mechanisms, was studied via integrated in vivo/vitro approaches. This study first reveals that lactic acid accelerates intervertebral disc degeneration by inducing cartilage endplate stem cells senescence and DNA damage, thereby activating the P16/P21/P53-centered senescence pathway. In a rat tail vertebra puncture-induced intervertebral disc degeneration model, degenerated discs exhibited increased lactic acid levels, narrowed intervertebral spaces, and disrupted nucleus pulposus structure (P<0.05). In vitro, 0/2/6/10 mM lactic acid dose-dependently suppressed cartilage endplate stem cells viability (10 mM group: 15.7% of the control), elevated intracellular reactive oxygen species (ROS, 2.8-fold relative to the control), induced G0 cell cycle arrest (10 mM group: 85.63%), reduced EdU-positive cells (8.62%), and increased {beta}-galactosidase-positive cells (10 mM group: 33.06%) and {gamma}-H2AX foci (all P<0.01).Molecularly, lactic acid significantly upregulated P16 (2.1-fold), P21 (3.1-fold), P53 (2.4-fold), and {gamma}-H2AX (1.8-fold). In vivo intervertebral disc injection confirmed a positive correlation between lactic acid concentration and intervertebral disc degeneration severity. This study clarifies lactic acids role in intervertebral disc degeneration via the "oxidative stress-cell cycle arrest-cellular senescence" axis, advancing understanding of intervertebral disc degeneration pathogenesis and providing a basis for targeted therapies against lactic acid metabolism.

cell biology↗

bioRxiv2026

Polymer-lipid hybrid nanoparticle enhances mRNA delivery and T cell-mediated immunity

mRNA vaccines have transformed prophylactic immunization against infectious diseases as well as therapeutic interventions for cancer. However, their effectiveness against emerging viral variants and a range of malignancies continues to be hindered by suboptimal induction of T cell-mediated immunity. To overcome this limitation, here we developed a polymer-lipid hybrid nanoparticle (PLNP) platform engineered to improve mRNA delivery to antigen-presenting cells (APCs) and to potentiate T cell responses. Relative to conventional mRNA lipid nanoparticle (LNP) vaccines, mRNA PLNP vaccines demonstrated markedly improved lymph node targeting, APC activation, Th1-biased pro-inflammatory cytokine response, and antigen-specific T cell expansion while retaining robust humoral immunity. Remarkably, mRNA-PLNP vaccines generated approximately 50% more antigen-specific CD8+ T cells than mRNA-LNP vaccines across multiple antigens, including SARS-CoV-2 spike, influenza hemagglutinin, and ovalbumin. In prophylactic applications, mRNA PLNP vaccine provided complete protection against SARS-CoV-2 variants. As a therapeutic approach in a melanoma model, mRNA PLNP vaccination resulted in enhanced tumor control and significantly prolonged survival compared to LNP-based formulations. Collectively, these results establish PLNP as a versatile and broadly applicable platform for augmenting mRNA vaccine efficacy through improved mRNA delivery and T cell priming, offering promising implications for infection prevention and cancer immunotherapy.

immunology↗

bioRxiv2026

A micropeptide component of the OGDH complex modulates ATP production in the TCA cycle

Since its elucidation, the tricarboxylic acid (TCA) cycle has been regarded as a fully defined enzymatic pathway. Here, we report the discovery of a previously unrecognized micropeptide component of this central metabolic system. Through analyzing ribosome profiling data from the mouse sORFs.org database, we discovered APPM (ATP production-promoting micropeptide), a 29-amino acid peptide encoded by a non-canonical small open reading frame within the mouse Ctsb gene. APPM localizes to the mitochondrial matrix and inner membrane, where it directly binds to the E1 subunit (OGDH) of the -ketoglutarate dehydrogenase complex (OGDHc). This interaction modulates OGDHc enzymatic activity, thereby regulating NADH and ATP production. We identified tyrosine-13 as the critical residue mediating the APPM-OGDH interaction and functional activation. Exogenous APPM administration increased ATP levels in vivo and, in a mouse model of heart failure, restored cardiac function, outperforming the reference drug trimetazidine. Collectively, our findings identify APPM as the first micropeptide regulator of the OGDH complex, expanding the known repertoire of the TCA cycle and presenting a potential therapeutic strategy for bioenergetic disorders.

molecular biology↗

bioRxiv2025

Multi-omics Analysis of Human Blood Cells Reveals Unique Features of Age-associated Type2 CD8 Memory T cells

Aging impacts immune function, but the mechanisms driving age-related changes in immune cell subsets remain unclear. To explore age-dependent changes in immune cell populations, we analyzed human peripheral blood mononuclear cells (PBMCs) from a cohort of healthy donors aged 20-82 years using a 36-color spectral flow cytometry panel focused on T cells. We identified a unique population of memory CD8 T cells, which lack CXCR3 and produce a Th2-like cytokine response, accumulate with age. We discovered an age-dependent bias in naive CD8 T cells toward Th2 cytokine production, accompanied by transcriptional and epigenetic changes supporting this phenotype. Moreover, health outcome association analysis linked the accumulation of these unique CXCR3- central memory CD8 T cells to asthma, chronic liver conditions, and type 2 diabetes. Together, our results support the model that an age-dependent drift in epigenetic regulation towards a Th2-like phenotype drives a pathogenic Th2-like immune population.

immunology↗

bioRxiv2025

PARP10 condensation inhibits viral infection via targeting NAD+ homeostasis

ADP-ribosylation is a critical post-translational modification mediated by diphtheria toxin-like ADP-ribosyltransferases (ARTDs). The human ARTD family comprises 17 members that catalyze either poly- or mono-ADP-ribosylation. However, the functions and regulatory mechanisms of many ARTD proteins remain poorly understood. Here, we uncover an antiviral role for PARP10 through its ability to form biomolecular condensates. Viral infection triggers PARP10 condensation, a process driven by multivalent homotypic interactions among the structured domains. We show that mono-ADP-ribosylation of PARP10 suppresses its condensation, serving as a negative feedback mechanism that regulates condensate dynamics and protein stability. PARP10 condensates exhibit enhanced enzymatic activity, leading to decreased NAD+ levels and disruption of NAD+ homeostasis, ultimately inhibiting viral replication. Our findings establish PARP10 condensation as a novel mechanism for ARTD enzyme compartmentalization, with significant implications for innate immunity and host defense.

cell biology↗

bioRxiv2025

Lung derived extracellular vesicles have distinct pro-repair effects, depending on the age of their source tissue

Many age-related lung diseases encompass aberrant repair mechanisms. To develop novel treatments for these diseases, it is critical to understand how biology and repair signals are altered in aged lungs. Extracellular vesicles (EVs) carry bioactive signals reflecting their source tissue; therefore, we used EVs derived from precision-cut lung slices (PCLS) as tools to investigate differences in lung biology and repair signals that occur upon ageing and injury. We compared the physicochemical properties and biological content of four groups of EVs, obtained from uninjured and injured, young and aged PCLS. Treatment with EVs obtained from young, uninjured (YU) PCLS decreased apoptotic cells in both young and aged spatially injured (AIR)-PCLS. YU EVs also increased the percentage of alveolar progenitor cells in aged AIR-PCLS, indicating that aged lungs retain the capacity to mount a repair response, if provided with the right biological cues. Small RNA sequencing revealed the miRNA content of each EV group is altered, depending on the physiological conditions of their source tissue. Bioinformatic analysis of the target genes regulated by differentially expressed miRNAs identified enrichment of genes required for lung development and repair. These findings pave the way for future therapeutic strategies to repair or regenerate aged lungs.

cell biology↗

bioRxiv2025

The Structural Basis for RNA Binding and Recognition of the Disordered Prion-Like Domain of TDP-43

Though the structural details of how RNA interacts with folded RNA-binding domains are well established, how intrinsically disordered regions (IDRs) found in a large fraction of RNA-binding proteins mediate contacts with RNA and if they contribute to binding specificity has not been extensively characterized. The human RNA-binding protein TDP-43 is associated with many RNA processing functions that require its predominantly disordered C-terminal domain (CTD) that forms disease-associated inclusions in ALS, and other neurodegenerative conditions. Here, we demonstrate that TDP-43 CTD directly interacts with RNA primarily via a region of the IDR composed of clustered positively charged residues. Large RNAs act as a multivalent scaffold for CTD monomers, inducing the -helical segment of TDP-43 CTD to form multimeric protein-protein structures. Additionally, we probe the nucleotide base and amino acid specificity of CTD-RNA interactions, showing that arginine, aromatic and polar residues display a preference for U and G nucleic acid bases over C and A. Finally, we probe the molecular basis for the strong binding interaction between TDP-43 and G4 quadruplex structures and discover similarly avid interactions with cytosine-rich DNA I-motifs. This work deepens our understanding of how disordered regions of proteins contribute to RNA recognition, drive function, and contribute to disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/695782v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f1d256org.highwire.dtl.DTLVardef@284c2forg.highwire.dtl.DTLVardef@1a1d715org.highwire.dtl.DTLVardef@2fbb1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Skin microbiome composition and function in the development of atopic diseases during infancy

BackgroundAtopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome. ObjectiveTo determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy. MethodsWe analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status. ResultsWithin AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae. At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae. Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity. ConclusionsInfant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.

microbiology↗

bioRxiv2025

Metaplasia Enables Stomach Colonization by Fusobacterium animalis

Infection with Helicobacter pylori is the major risk factor for gastric cancer worldwide; yet the exact mechanisms behind this link remain unclear. H. pylori-associated tissue changes often disrupt the gastric microbiome, enabling secondary gastric colonization by oral bacteria. Among these secondary colonizers, Fusobacterium species have documented associations with several gastrointestinal cancers. We found that both F. animalis and F. nucleatum invade cultured human gastric adenocarcinoma cells, but F. animalis exhibited higher adherence and invasion, and hypoxic conditions promoted higher bacterial survival. Both adherence and invasion were inhibited by exogenous GalNAc, a glycan commonly observed in membrane glycoproteins of adenocarcinoma cells, and a target of the fusobacterial adhesin Fap2. Using a mouse model of gastric metaplasia, we found that F. animalis colonized gastric tissue only after metaplasia onset, growing in multispecies biofilms in the mucus layer, while F. nucleatum colonized neither healthy nor metaplastic gastric tissue. Metaplasia led to upregulation of Gal-GalNAc in the stomach, and reduced gastric acidity allowed higher F. animalis loads in this model. By contrast, inflammation and the presence of H. pylori did not significantly influence stomach colonization by F. animalis. Overall, our data support a model in which H. pylori-induced metaplasia makes the stomach susceptible to secondary infection by another cancer-associated microbe, F. animalis.

microbiology↗

bioRxiv2025

A high-throughput methods SNIPR-Nm reveals small RNA methylation ratio

Small RNAs regulate gene expression and genome stability, and their functions are shaped by 3'-terminal 2'-O-methylation (Nm). Although Nm is universal in plants and mainly marks animal piRNAs, recent evidence reveals Nm on mammalian miRNAs, highlighting broader regulatory roles. However, current sequencing underestimates Nm-modified RNAs due to ligation bias, and existing qPCR-based methods cannot simultaneously quantify abundance and modification, leaving Nm dynamics largely unexplored. We developed a unified enzymatic strategy that integrates poly(A) polymerase and a thermostable ligase to measure both small RNA abundance and 3'-end Nm status. Applied to mouse testis, it enables robust quantification of Nm ratios for piRNAs and miRNAs. Our method offers a versatile tool for dissecting small RNA methylation in development and disease.

genetics↗

bioRxiv2025

RNA modulates FUS condensate assembly, dynamics, and aggregation through diverse molecular contacts

Fused in sarcoma (FUS) is an RNA-binding protein that undergoes phase separation with RNA and other cellular components, forming ribonucleoprotein (RNP) granules. While recent advances delineating the molecular forces that underlie phase separation have largely focused on protein-protein interactions (1-6), the molecular details of protein-RNA interactions within condensates remain limited. In this study, we demonstrate that RNA modulates the phase separation of the low-complexity (LC) and arginine-glycine-glycine motif (RGG1) domains of FUS: low RNA concentrations enhance protein phase separation and excess RNA disrupts it. By integrating biochemical assays, NMR spectroscopy, and molecular dynamics simulations, we show that RNA incorporates into FUS condensates, reducing condensate density while enhancing local relaxation and diffusional motion of FUS. Surprisingly, whereas RNA binding in the dispersed phase primarily involves the RGG1 domain, within the condensed phase, both LC and RGG1 domains contribute to interactions with RNA. NMR and simulation data show diverse interactions between amino acids and RNA moieties, including prominent glutamine-RNA contacts, that stabilize FUS-RNA co-condensates. Furthermore, we found that RNA accelerates the liquid-to-solid transition of FUS LC-RGG1 condensates, promoting fibrillar aggregate formation. Together, these results provide mechanistic insight into how RNA regulates the assembly, dynamics, and maturation of protein condensates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/694118v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@19168a9org.highwire.dtl.DTLVardef@16e6878org.highwire.dtl.DTLVardef@18cb8a9org.highwire.dtl.DTLVardef@1af6a4c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Using NMR and molecular simulations, we map how RNA engages FUS LC-RGG1 within condensates through electrostatic, {pi}-stacking, and hydrogen-bond contacts. We find that RNA incorporation dilutes condensate density, tunes protein mobility, remodels interaction networks, and accelerates the formation of fibrillar aggregates. C_FIG

biochemistry↗

bioRxiv2025

Structural basis of Retron-Eco8-mediated anti-phage defense

Retrons represent a novel class of bacterial defense systems that employ reverse transcriptase (RT), non-coding RNA, and effector proteins to counteract phage infections. In this study, we elucidate the molecular mechanism of a retron system, Retron-Eco8. Biochemical experiments reveal that the Retron-Eco8 holocomplex, rather than the effector alone, exhibits double-stranded DNA cleavage activity in an ATP-independent manner, triggering abortive infection and effectively halting phage propagation. Cryo-electron microscopy (cryo-EM) analysis reveals a supramolecular assembly comprising four RT subunits, four msDNA (multicopy single-stranded DNA) molecules, and four OLD (overcoming lysogenization defect) nucleases--a configuration critical for anti-phage defense. Structural comparisons between apo and ATP-Mg2+-bound states demonstrate a local conformational change. Notably, we identify the phage SSB (single-stranded DNA-binding) protein as an activator of Retron-Eco8, and phylogenetic analysis of SSB proteins further elucidates the phage resistance specificity. Collectively, our findings delineate the structural architecture of the Retron-Eco8 defense complex and provide mechanistic insights into retron-mediated bacterial immunity.

biophysics↗

bioRxiv2025

Therapeutic Potential of Neural Rosette Stem Cell-Derived Small Extracellular Vesicles in the Management of Brain Edema

Small extracellular vesicles (sEVs) derived from neural stem cells (NSCs) have gained significant interest for their potential roles in neuroprotection, brain edema management, and the preservation of blood-brain barrier (BBB) integrity. These nanoscale particles facilitate intercellular communication and carry a diverse array of bioactive molecules, including proteins and RNAs, which influence various neurobiological processes. The composition of their cargo depends on the parental cell type, affecting their interactions with recipient cells. In this study, we characterized the cargo of sEVs derived from neural rosette stem cells (NRSCs) at both transcriptomic and proteomic levels and compared it to sEVs derived from cardiomyocyte progenitor cells (CMPCs) and human pluripotent stem cells (hPSCs). Furthermore, we assessed the therapeutic effects of NRSC-derived sEVs in a rat model of transient middle cerebral artery occlusion (tMCAO) to investigate neuronal injury and the progression of brain edema. Our proteomic and miRNA analyses revealed that the sEVs from NRSCs, CMPCs, and hPSCs possess distinct cargo compositions. In an in vitro neuronal ischemia model, NRSC-derived sEVs significantly enhanced cell viability, while in an endothelial model, they expedited the restoration of cell barrier integrity. Furthermore, the in vivo studies utilizing the rat model of tMCAO showed that intravenous administration of NRSC-derived sEVs at 3, 24 and 48 hours after reperfusion resulted in a significantly faster resolution of brain edema. These findings underscore the influence of the parental cell type on sEV composition and highlight the therapeutic potential of NRSC-derived sEVs in treating brain edema, paving the way for novel therapeutic strategies.

neuroscience↗