Biology subjects

Guo, L.

Publications and source records attributed to Guo, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Telomere-to-telomere gap-free and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome sequence remains incompletely assembled. We report a 4.2Gb telomere-to-telomere gap-free N. tabacum reference genome phased into two subgenomes (subS/subT) , revealing differential evolutionary trajectories between two subgenomes marked by a rapid divergence in paternal T-genome, especially for heterochromatic centromeric regions. To understand the evolutionary dynamics of tobacco centromeres following polyploidization, we characterize the centromere architecture in tetraploid N. tabacum and its diploid progenitors, demonstrating clear subgenomic diversification and repositioning of centromeres during speciation and allopolyploidization. These findings enrich our knowledge on centromere paradox in polyploid genomes.

genomics↗

bioRxiv2026

High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation

The de novo design of high-affinity protein binders remains a central challenge in protein engineering and therapeutic discovery. While deep generative models have advanced backbone generation and interface design, achieving picomolar or nanomolar binding affinities typically demands extensive experimental screening or iterative in vitro maturation. A general computational approach for the direct production of high-affinity binders has remained elusive. Here, we introduce an integrated framework that synergizes PPIFlow, a flow-matching-based generative model, with a novel in silico maturation strategy. PPIFlow employs a pairformer architecture to explicitly reason over pair-wise geometric and chemical interactions, modeling protein backbone rigid-body transformations as continuous flows. To bridge the affinity gap, we implement a dedicated in silico affinity maturation stage that combines interface rotamer enrichment with partial flow refinement to optimize energetic packing. This pipeline is further accelerated by AF3Score, a score-only adaptation of AlphaFold3 that enables high-fidelity and computationally efficient candidate prioritization. Across a diverse set of therapeutic targets, this synergistic approach consistently produces picomolar and nanomolar affinity binders without experimental affinity maturation. Notably, the framework proves highly effective for the de novo design of single-domain antibodies (VHHs), producing sub-nanomolar binders across multiple targets. These results establish that coupling robust backbone generation with focused in silico maturation renders the purely computational design of high-affinity binders feasible.

biochemistry↗

bioRxiv2026

Genomic and pan-genomic insight into longan domestication and improvement

Longan (Dimocarpus longan) is a tropical tree in Sapindaceae family with economic importance known for its nutritous fruits. Genetic improvement of longan requires knowledge of reliable molecular markers and functional genes associated with key traits. However, it is largely impeded by lacking a complete genome and pangenome reference encompassing the broad genetic diversity in diverse longan germplasms. Here, we present a telomere-to-telomere (T2T) gap-free genome of longan cultivar Shixia and a graph-based pangenome constructed using newly assembled chromosome-level genomes of 101 accessions. We completely assemble the longan centromere regions primarily composed of Gypsy-CRM retrotransposons. The pan-genome analysis reveals 58,978 non-redundant structural variants (SVs) that exhibit signs of genomic selective sweep during longan domestication and breeding. Additionally, haplotype-resolved genome analysis suggests allele-specific gene expression associated with SV-driven changes in 3D genome architecture. Importantly, the graph-based pan-genome empowers population-scale SV genotyping and genomewide association with various longan traits. SV-GWAS revealed 12 QTLs significantly linked with longan maturity period. Among them, a 758bp insertion is located downstream of the DlDAZ gene encoding a C2H2 zinc-finger transcription factor, and DIDAZ-transgenic tomatoes showed delayed maturity. Together, our T2T genome and pan-genome provide valuable resources to facilitate longan genetic research and precise improvement.

genomics↗

bioRxiv2025

An Integrated Single-Cell Atlas Reveals Hepatic Stellate Cell Heterogeneity and Spatiotemporal Dynamics after Liver Injury

BackgroundHepatic stellate cells (HSCs) orchestrate fibrosis-free repair after acute liver injury (ALI) and sustain fibrogenesis in chronic liver injury (CLI). However, the heterogeneity and spatiotemporal dynamics of HSCs across these different injury models remain elusive. This study sought to construct a cross-etiological HSC atlas to delineate HSC states and transitions during liver injury. MethodsWe integrated 86,072 single-cell transcriptomes from 84 mouse samples across four etiologies and validated findings using multi-omics data from 277 mouse and 798 human samples. Cellular dynamics were characterized through clustering, trajectory inference, spatial analysis, and multicellular coordination network analysis. Experimental validation included liver injury models and gain-of-functional assays in primary mouse HSCs and LX-2 cells. ResultsWe established a cross-etiological, spatiotemporally resolved HSC atlas comprising 11 subpopulations. Trajectory analysis delineated a continuous quiescence-activation-attenuation (QAA) trajectory, recapitulating the in vivo full spectrum of state transitions and being supported by sequential pathway activation validated in vitro. In ALI, HSCs spatiotemporally completed the QAA trajectory around injury zones, whereas collagen-producing S100a6 HSCs pathologically accumulated in mouse and human CLI due to trajectory dysregulation. Notably, the atlas identified a previously unrecognized apoptosis-prone Mrc2 HSC subtype strongly co-localized with p53 in both mice and humans. Overexpression of transcription factors confirmed that Hbp1, Tbx20, Atoh8, and Plagl1 enriched in Mrc2+ HSCs promoted HSC apoptosis. Finally, we revealed the microenvironment of distinct cellular modules which coordinated HSC progression along the QAA trajectory. A 531-gene signature derived from the inflammatory-fibrotic cellular module significantly correlated with fibrosis stage and hepatocellular carcinoma risk in human cohorts. ConclusionsWe established a comprehensive HSC atlas and delineates HSC heterogeneity and spatiotemporal dynamic across etiologies. Dysregulation of the QAA trajectory underlies fibrotic progression, providing a resource for identifying antifibrotic targets.

cell biology↗

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

Elevated plasma cholesterol causally improves sepsis outcome by promoting hepatic metabolic reprogramming

RationaleSepsis is a life-threatening condition with high mortality and limited therapeutic options. While hypocholesterolemia is associated with poor outcomes, the causal role of cholesterol and its underlying mechanisms remain unclear. ObjectivesTo determine whether elevated plasma cholesterol improves sepsis survival and to elucidate the mechanistic basis of this effect. MethodsWe analyzed septic patients from the MIMIC-IV database. Total cholesterol levels were compared between 28-day survivors and non-survivors using Wilcoxon rank-sum tests. Cox proportional hazards regression assessed the association between cholesterol levels and mortality, adjusting for age, sex, race, SOFA score, and Charlson comorbidity index. To establish causality, C57BL/6J mice were randomized to receive either a high-cholesterol diet (HCD) or regular diet (RD) for three days prior to cecal ligation and puncture (CLP) to induce sepsis. Measurements and Main ResultsSurvivors had significantly higher cholesterol levels than non-survivors (median, 135 vs. 126 mg/dL, p < 0.001). High cholesterol ([≥] 133 mg/dL) was independently associated with reduced 28-day mortality (adjusted HR = 0.80, 95% CI: 0.67-0.95, p = 0.012). In mice, HCD elevated plasma cholesterol and significantly improved survival (52.5% to 90%), independent of immune modulation.Hepatic transcriptomics revealed metabolic reprogramming, including upregulation of oxidative phosphorylation and glutathione-mediated antioxidant pathways, and suppression of endoplasmic reticulum proteostasis. Notably, inhibition of mitochondrial respiration abolished the survival benefit. ConclusionsElevated plasma cholesterol causally improves sepsis outcomes by promoting hepatic metabolic reprogramming. These findings offer mechanistic insight into clinical observations and suggest hepatic bioenergetics as a novel therapeutic target in sepsis.

physiology↗

bioRxiv2025

The Janus face of Selinexor (KPT-330) in bacterial infection: short-term protection versus long-term lethality

The clinical application of the anti-cancer drug KPT-330 (Selinexor) has been associated with increased infection-related mortality, yet its direct impact on infection pathogenesis remains unclear. Here, we found that KPT-330 treatment reduced host survival from 66% to 22% in a mouse model of bacterial pneumonia. Interestingly, KPT-330 conferred transient lung protection at 24 h post infection by blocking the nuclear export of I{kappa}B, suppressing NF{kappa}B signaling and immune cell recruitment. Meanwhile, KPT-330 induced apoptosis of lung epithelial cells, enhancing bacterial adhesions and invasion, and leading to dramatically increased bacterial load. These effects culminated in a compensatory immune rebound and more severe lung injury at later stages. Adjunctive therapy with the antibiotic polymyxin E (colistin) rescued survival, whereas the immunosuppressant dexamethasone did not, underscoring that timely bacterial clearance is critical for managing this adverse effect. Our findings provide direct evidence that KPT-330 exacerbates bacterial infection and advocate for an adjunctive antimicrobial prophylaxis strategy to ensure its safer use, especially in high-risk patients.

microbiology↗

bioRxiv2025

REST elevation-dependent chromatin remodeling and alternative Grk6 transcript synthesis hyperactivates Cxcr4-Sdf1 signaling in cerebellar granule cell progenitors

RE1 Silencing Transcription Factor (REST) is a repressor of transcriptional initiation of genes involved in neurogenesis. Here, we show that conditional REST elevation in cerebellar granule cell progenitors (CGNPs) of RESTTG mice perturbed foliation, increased cell migration, and sustained C-X-C motif receptor 4 (Cxcr4) signaling, a pathway key to postnatal CGNP migration. Mechanistic studies uncovered a novel role for REST in controlling transcript diversity and exon skipping in CGNPs. Alternative transcript expression was detected in known Cxcr4 signaling regulator, G-protein-coupled receptor kinase-6 (Grk6). Further analysis of Grk6s isoform expression revealed an upregulation of a transcript lacking exon 10a (Grk6-207) in RESTTG CGNPs. Grk6-207 expression in wildtype CGNPs hyperactivated Cxcr4 signaling and increased chemotaxis. Structural modeling of Grk6-207 predicted changes in active site conformation and interactions with Cxcr4 and {beta}-Arrestin-1, supporting impairment of Cxcr4 signaling desensitization. Interestingly, REST elevation promoted increased chromatin accessibility at the exon10a-10b junction and exon 10a exclusion. Integrated multiomic analyses identified the enhancer of zeste (Ezh2) as a potential mediator of alternative transcript generation which demonstrated increased occupancy at the exon10a-10b locus in RESTTG CGNPs. Pharmacological inhibition of Ezh2 downregulated Grk6-207, confirming a role for Ezh2 in Grk6 exon10a exclusion and the increased migration in RESTTG CGNPs. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/682654v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@166db32org.highwire.dtl.DTLVardef@1c0c5e0org.highwire.dtl.DTLVardef@ff2d6borg.highwire.dtl.DTLVardef@fed170_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

IGP receptors act as redox sensors to mediate broad-spectrum disease resistance induced by cellooligomers

Cys-oxidation is a well-established post-translational regulator of intracellular protein function, yet its role in extracellular receptor-mediated signaling remains poorly understood. Here, we investigate the LRR-Malectin receptor-like kinase IGP1, a key receptor for plant cell wall damage-associated molecular patterns (DAMPs). We demonstrate that IGP1 directly recognizes cellooligomers with a degree of polymerization [≥] 3 via a conserved binding groove in its LRR domain, not the malectin domain as anticipated. Strikingly, a pair of cysteines within the malectin domain functions as a redox sensor, undergoing hydrogen peroxide-induced oxidation that sterically reduces ligand binding affinity and attenuates immune signaling. Phylogenetic analyses reveal that IGP originated after the terrestrialization of plants, and is an evolutionarily conserved redox sensor in land plants. Functional studies in Arabidopsis (Arabidopsis thaliana), wheat (Triticum aestivum), and soybean (Glycine max) confirm that the IGP-cellooligomer module confers broad-spectrum disease resistance. Our work uncovers a unique mechanism where ligand perception and redox sensing are integrated into a single receptor to regulate DAMP-triggered immunity.

plant biology↗

bioRxiv2025

Association of cytochrome c oxidase dysfunction with amyloidosis in Alzheimer's disease and patient-derived cerebral organoids

Patients with Alzheimers disease (AD) demonstrate brain mitochondrial dysfunction and energy deficiency that are closely associated with cognitive impairment. Cytochrome c oxidase (CCO), also known as mitochondrial complex IV, is the terminal enzyme in mitochondrial electron transport chain (ETC). Consistent with the pivotal role of CCO in mitochondrial bioenergetics and high demand for energy to sustain neuronal function, CCO dysfunction has been linked to neurological disorders including AD. However, it remains unclear whether mitochondrial CCO dysfunction represents an adaptive response to AD-associated toxic molecules versus a bona fide pathology to promote AD development. In this study, by meta-analysis of publicly available proteomics analysis of post-mortem frontal lobe tissues from four large cohorts of patients with AD we identified loss of key CCO subunits including mitochondrial DNA (mtDNA)-encoded COX1 and COX3 as well as nuclear DNA (nDNA)-encoded COX5A, COX6B1, COX7C, COX8A, and NDUFA4 in patients with AD. Further biochemical analysis using post-mortem frontal lobe tissues showed lowered CCO activity of neuronal mitochondria from patients with AD, suggesting CCO vulnerability and its potential association with amyloidosis in AD. Lastly, in addition to the inverse relationship between neuronal CCO activity and brain amyloidosis in the tested AD cohort, pharmacological inhibition of CCO promoted amyloid production and elevated beta-secretase 1 (BACE1) activity in cerebral organoids derived from human induced pluripotent stem cells (hiPSCs) from one nonAD and one AD subject. The simplest interpretation of the results is that CCO dysfunction in the frontal lobe is a phenotypic mitochondrial change accompanying AD, which may contribute to the development of brain amyloidosis.

neuroscience↗

bioRxiv2025

Gliomas phenocopy an inborn error of metabolism to drive neuronal activity and tumor growth

The metabolic hallmarks of high-grade glioma (HGG) are not fully understood. Human brain tissue metabolomics revealed that the creatine synthesis pathway intermediate guanidinoacetate (GAA) accumulated [~]100-fold in HGGs relative to controls, which was caused by imbalanced activities of enzymes in this pathway. Glioma cells secreted GAA rather than using it to produce creatine, implicating an unexpected function. GAA accumulates in GAMT deficiency, an inborn error of metabolism, and elevates neuronal excitability. Neuronal excitability is also increased in glioma and drives tumor growth through neuron-glioma interactions. We hypothesized that glioma-generated GAA excites surrounding neurons. Indeed, GAA induced neuronal hyperactivity by activating GABAA receptors and causing depolarizing GABA currents in glioma-associated neurons with dysregulated chloride homeostasis. Depleting tumoral GAA decreased electrochemical activity, neuron-glioma interactions, and tumor aggressiveness. Our findings unveil a new mechanism linking cancer metabolism with cancer neuroscience and leverage human genetics to nominate GAA synthesis as a target in gliomas.

cancer biology↗

bioRxiv2025

Sleep Deprivation Primes Synaptic Vulnerability Without Inducing Oxidative Damage: A Mechanistic Reappraisal

The question of whether sleep deprivation is inherently lethal has remained unresolved due to the inability to separate pure sleep loss from experimental stress. Historical studies dating back over a century have consistently reported that prolonged wakefulness leads to death, but these findings have been confounded by the stressful nature of the experimental interventions used to maintain wakefulness. Recent work has suggested that sleep deprivation-induced lethality may result from accumulation of reactive oxygen species (ROS) in the intestines, providing a potential molecular explanation for these long-standing observations. Here we address whether lethality stems from sleep loss itself or experimental stress using stress-controlled sleep deprivation in Drosophila and stress paradigms in both flies and mice. Using real-time feedback-controlled sleep deprivation in Drosophila--which only stimulates animals when they attempt to sleep--we found no lethality or intestinal ROS accumulation even after 240 hours of continuous wakefulness. In contrast, both physical perturbation and psychological challenges rapidly induced intestinal ROS accumulation independent of sleep loss, in flies and mice. Transcriptomic analysis revealed entirely distinct molecular signatures between sleep deprivation and oxidative stress, demonstrating these represent fundamentally different biological challenges. However, while sleep deprivation alone caused no lethality or intestinal oxidative stress, it increased susceptibility to traumatic brain injury through enhanced synaptic strength. Sleep-deprived flies showed increased mortality when subjected to violent physical challenges, an effect that correlated with synaptic excitability rather than sleep duration, and was rescued by restorative recovery sleep or prevented in mutants lacking synaptic potentiation mechanisms. Our findings demonstrate that experimental stress, not sleep loss, drives the oxidative damage and lethality historically attributed to sleep deprivation. Sleep deprivation, however, creates conditional vulnerability by transforming the brain into a hyperexcitable state susceptible to trauma, rather than causing cumulative damage.

neuroscience↗

bioRxiv2025

Distinct Electrophysiological Signatures Define Neuronal Subtypes in the Fasciola Cinereum

The fasciola cinereum (FC) is a small, conserved hippocampal subregion whose cellular properties remain poorly understood. Anatomically positioned between dorsal CA1 and the third ventricle, the FC receives diverse cortical and subcortical inputs but is often excluded from hippocampal circuit models. Here, we performed ex vivo whole-cell patch-clamp recordings in mouse hippocampal slices to define the intrinsic and synaptic properties of FC neurons. We find that FC neurons are electrophysiologically and morphologically distinct from neighboring CA1 and CA2 pyramidal cells, exhibiting reduced intrinsic excitability, delayed spike initiation, and enhanced afterhyperpolarizations. These properties are strongly shaped by potassium conductances, with Kv2 (KCNB) and Kv7 (KCNQ) channels contributing to the suppression of firing. We find that FC neurons span a continuum of intrinsic excitability which is structured by variability in potassium channel-mediated conductances and is inversely coordinated with excitatory synaptic input, such that less excitable neurons receive stronger synaptic drive. Together, these findings establish a mechanistic framework in which intrinsic membrane properties and synaptic input are co-organized across the FC population, providing new insight into how this understudied hippocampal region may contribute to the regulation of neural excitability. Key PointsO_LIThe fasciola cinereum (FC) is a small and poorly understood hippocampal subregion that has recently been implicated in hippocampal related function and seizure activity. C_LIO_LIHere we show that neurons in the FC are morphologically and functionally distinct from cells in neighboring CA1 and CA2 hippocampal subregions, and find substantial physiological diversity of FC neurons, including differences in firing behavior, membrane properties, and intrinsic excitability. C_LIO_LIPharmacological analyses show that Kv2 and Kv7 potassium channels play a key role in shaping the intrinsic properties of FC neurons. C_LIO_LILess excitable FC neurons receive stronger excitatory synaptic input, revealing an inverse relationship between intrinsic membrane excitability and synaptic drive. C_LIO_LIThese findings identify the FC as a physiologically specialized hippocampal subregion and provide a foundation for understanding its role in hippocampal function and neurological disease. C_LI

neuroscience↗

bioRxiv2025

Mutant IDH silences GSX2 to reprogram neural progenitor cell fate and promote gliomagenesis

Isocitrate dehydrogenase (IDH) mutations arise early in gliomas and are associated with a defined neurodevelopmental cancer cell hierarchy. However, how mutant IDH contributes to this hierarchy and whether this interaction promotes gliomagenesis remain unclear. We captured the dynamics of IDH-mutant glioma initiation in genetically engineered mice through time-resolved, single-cell genomics. Mutant IDH activates and induces lineage switching of neural progenitor cells (NPCs). These actions expand oligodendrocyte precursor cells, the predominant cell-of-origin for these tumors, at the expense of interneurons. Lineage switching is mediated by promoter hypermethylation and silencing of Gsx2, a homeobox gene required for neurogenesis. Critically, Gsx2 ablation recapitulates NPC fate reprogramming by mutant IDH. We provide a new model of neural cell fate control by IDH oncogenes and insights into the developmental origins of glioma.

cancer biology↗

bioRxiv2025

Haplotype-resolved T2T gap-free genomes of the winegrape cultivar 'Cabernet Sauvignon'

Cabernet Sauvignon (CS), a cultivar of winegrape (Vitis vinifera), is among the most renowned winegrape varieties globally. In this study, we released the haplotype-resolved telomere-to-telomere (T2T) CS genome assembled using a combination of PacBio HiFi, ONT ultra-long, and Hi-C sequencing data. The two T2T gap-free haplotype-resolved assemblies CS-T2T.Hap1 and CS-T2T.Hap2 sized 491.11 Mb (contig N50 = 25.09 Mb) and 491.90 Mb (contig N50 = 25.51 Mb), respectively. Genome annotation predicted a total of 36,456 genes in CS-T2T.Hap1 and 35,471 genes in CS-T2T.Hap2. By genome comparison, we discovered and validated megabase inversion events on Chromosome 03,11,18 and 19, which are not prevalent in other haplotype-resolved V. vinifera genomes. In summary, this haplotype-resolved T2T genome represents an essential genomic resource for Cabernet Sauvignon, and lays the foundation for its genetic studies, improvement and utilization.

genomics↗

bioRxiv2025

A high-quality bread wheat genome unravels adaptive evolution of wheat end-use quality

Understanding the genetics of superior dough performance is essential for improving wheat end-use quality. Here, we presented a de novo assembly of the genome of JM44, a Chinese wheat cultivar known for its exceptional end-use quality. The JM44 genome achieved reference-level quality (QV = 66.74), depicting a complete picture of complex regions containing gluten genes. Our microsynteny analysis across the Triticum-Aegilops complex showed that high-molecular-weight glutenin subunits (HMW-GSs) loci are highly conserved, while low-molecular-weight glutenin subunits (LMW-GSs) and -/{beta}-gliadins exhibited greater structural variation. These variable loci appear to have been preferentially selected by humans and contributed substantially to the evolution of wheat quality traits. Moreover, we observed that epistatic interactions between gluten genes are strong in modern cultivars, but markedly weaker in landraces, indicating the importance of epistatic selection during modern breeding. Our findings shed light on the genomics and evolution of wheat quality traits, providing valuable guidance for future breeding efforts.

genomics↗

bioRxiv2025

Human ribosome interactions reframe neomycin toxicity

Aminoglycosides such as neomycin are clinically limited by toxicity, commonly attributed to the inhibition of mitoribosomes. Here, we re-evaluate this mechanism by integrating Cryo-EM and functional assays to assess neomycins binding potential in vitro with its cellular engagement and functional consequences. Cryo-EM revealed extensive multi-site binding of neomycin on both human mitochondrial and cytosolic ribosomes in vitro, including conserved regions of the decoding center. In contrast, ribosomes isolated from neomycin-treated cells show markedly remodeled occupancy patterns, with no detectable neomycin bound to the mitoribosomes and reduced occupancy at a subset of cytosolic ribosome sites. However, neomycin remained functionally active in cells, inducing widespread stop-codon readthrough while having minimal effects on global mitochondrial and cytosolic protein synthesis. These findings reveal a disconnect between structural binding potential and cellular target engagement and identify disruption of translational fidelity, rather than global translational inhibition, as a major cellular consequence of neomycin exposure.

biochemistry↗

bioRxiv2025

Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes

Tibetan antelopes, native to high-altitude plateau regions, play a vital role in the local ecosystem. However, their gut microbiota harbors diverse antibiotic resistance genes (ARGs) and virulence genes (VFGs), raising concerns about the potential spread of antibiotic resistance in wildlife. In this study, in addition to collecting 26,608 metagenome-assembled genomes (MAGs) from public databases, we performed gut metagenomic sequencing on 68 Tibetan antelopes and obtained 7,318 MAGs through binning. A total of 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being the most prevalent. Comparative analysis revealed 7 ARGs unique to Tibetan antelopes, suggesting species-specific adaptations. Additionally, during the analysis of shared antibiotic resistance profiles between Tibetan antelopes and humans, two bacterial strains were identified within the Tibetan antelope gut microbiota: Enterococcus gallinarum exhibiting resistance to extended-spectrum class A beta-lactamases and Klebsiella grimontii demonstrating vancomycin resistance. Mobile genetic elements played a key role in ARG dissemination. ARGs were significantly correlated with VFGs, particularly those linked to adherence and effector delivery systems. These findings underscore for the first time the potential ecological and health implications of ARG dissemination in Tibetan antelopes, highlighting the need for further surveillance to assess its impact on wildlife and environmental resistomes.

microbiology↗