Biology subjects

xu, s.

Publications and source records attributed to xu, s..

7 recordsLinked to original sources

bioRxiv2026

Manganese Ion Inhibits Influenza A Virus Replication by Targeting the PA Endonuclease

Influenza A virus remains a major global health threat, with rapid mutation and emerging drug resistance underscoring the urgent need for novel antivirals. Manganese ions (Mn2+) are known to enhance host antiviral immunity, but their direct effects on influenza virus replication remain elusive. Here, we demonstrate that manganese chloride (MnCl2) potently inhibits the replication of both H1N1 and H3N2 subtypes in cultured cells at micromolar concentrations, with antiviral activity not shared by other divalent cations (Ca2+, Cu2+, Zn2+, Mg2+). Mechanistically, MnCl2 acts predominantly at post-entry stages, suppresses viral mRNA synthesis, and directly inhibits the RNA cleavage activity of the PA endonuclease. Pharmacological antagonism with the PA inhibitor baloxavir further supports PA as a key target. In a mouse model, intranasal MnCl2 administration alleviated body weight loss, reduced mortality, and decreased pulmonary viral RNA loads. Collectively, these findings identify Mn2+ as a direct inhibitor of influenza virus replication that acts, at least in part, by targeting the PA endonuclease, providing a conceptual framework for metal ion-based antiviral strategies.

microbiology↗

bioRxiv2025

HPV16 E2 protein possesses intrinsic helicase activity and sterically hinders E1 function through direct interaction

HPV16 E2 protein is a key regulatory protein essential for viral replication, yet no enzymatic activity had been attributed to it until now. In this study, we report for the first time that E2 possesses intrinsic ATP-dependent DNA unwinding activity. Mutational analysis identified residues K299, Y303, and K306 as critical for this helicase function. We further demonstrate that podophyllotoxin directly binds to E2 and inhibits its unwinding activity with an IC50 of 0.1074 {micro}M, mediated primarily by residues Q320 and H342. Comparative analysis revealed that the ATPase and helicase activities of E2 are considerably weaker than those of E1. Notably, we discovered that E2 potently inhibits the helicase activity of E1. This suppression is facilitated by the N-terminal domain of E2 (amino acids 1-245) through direct interaction with E1, with residue E39 playing a critical role. Our findings not only unveil a previously unrecognized enzymatic function of E2 but also suggest its role as a potential antiviral target. Moreover, the observed inhibitory effect of E2 on E1 highlights a novel regulatory mechanism for HPV DNA replication. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/676238v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@12fd0aforg.highwire.dtl.DTLVardef@2dc50forg.highwire.dtl.DTLVardef@e46f5eorg.highwire.dtl.DTLVardef@14b87da_HPS_FORMAT_FIGEXP M_FIG C_FIG E2 protein has traditionally been recognized primarily for its DNA-binding and transcriptional regulatory functions. This study provides the first evidence that E2 protein possesses intrinsic enzymatic activity, identifies a small-molecule inhibitor targeting this activity, and reveals a novel mechanism of E1-E2 interaction. O_LIHPV16 E2 Protein Exhibits ATPase and Helicase Activities C_LIO_LIIdentification of Key Amino Acid Residues for HPV16 E2 Protein Enzymatic Activity C_LIO_LIPPT Effectively Inhibits E2 Protein Helicase Activity In Vitro C_LIO_LIE2 Protein Exhibits Weaker Enzymatic Activity Than E1 and Inhibits E1 Helicase Activity C_LIO_LIE2 Inhibits E1 Helicase Activity Through Protein-Protein Interaction C_LI

molecular biology↗

bioRxiv2025

FGF8 promotes lipid droplet accumulation via the FGFR1/p-p38 axis in chondrocytes

Chondrocytes store lipids in the form of lipid droplets (LDs) and maintain cartilage lipid metabolic homeostasis by consuming or regenerating LDs. This modulation is largely mediated by a series of biochemical factors. Fibroblast growth factor 8 (FGF8) is one of the most important factors involved in the proliferation, differentiation, and migration of chondrocytes, and has attracted increasing attention in the physiology and pathology of cartilage. However, the effect of FGF8 on LD accumulation in chondrocytes remains unclear. This study aimed to elucidate the role of FGF8 in LDs and explore the underlying biomechanism involved. The results showed that FGF8 promoted LD accumulation in chondrocytes by upregulating perilipin1 (Plin1) expression. FGF8 activates the cytoplasmic p-p38 signaling pathway via fibroblast growth factor receptor 1 (FGFR1) to increase LD accumulation in chondrocytes. Subsequent experiments with siRNAs and specific inhibitors further confirmed the importance of the FGFR1/p38 axis for LD accumulation in chondrocytes exposed to FGF8. These results increase our understanding of the role of FGF8 in the lipid metabolic homeostasis of chondrocytes and provide insights into the physiology and pathology of cartilage.

cell biology↗

bioRxiv2025

The Role of Microglia and Complement C5/C5a in the Pathogenesis of Rhegmatogenous Retinal Detachment with Choroidal Detachment

BackgroundRhegmatogenous retinal detachment with choroidal detachment (RRDCD) is an uncommon and sight-threatening disorder marked by fast development and significant inflammation. This study aimed to identify cellular and molecular signatures distinguishing RRDCD from typical rhegmatogenous retinal detachment (RRD) and to investigate the roles of microglia and the complement C5/C5a pathway in disease pathogenesis. MethodsSingle-cell RNA sequencing (scRNA-seq) was employed to analyze vitreous samples from patients with RRD and RRDCD, indicating its involvement in blood-retina barrier impairment. ResultsOur findings revealed a distinct cellular landscape in RRDCD, characterized by enhanced connectivity between microglia and dendritic cells, alongside a significant upregulation of the complement C5-C5AR1 interaction. In vitro experiments indicated that treatment with complement C5 promoted microglial proliferation and activation, induced apoptosis in RF/6A endothelial cells, and disrupted tight junctions in ARPE-19 epithelial cells, suggesting a role in blood-retina barrier dysfunction. ConclusionThe findings substantiate the inflammatory hypothesis regarding the pathogenesis of RRDCD, emphasizing the critical functions of microglia and the complement C5/C5a pathway in intensifying retinal inflammation and undermining vascular integrity.

bioinformatics↗

bioRxiv2024

Workflow enhancement of TurboID-mediated proximity labeling for SPY signaling network mapping

TurboID-based proximity labeling coupled to mass spectrometry (PL-MS) has emerged as a powerful tool for mapping protein-protein interactions in both plant and animal systems. Despite advances in sensitivity, PL-MS studies can still suffer from false negatives, especially when dealing with low abundance bait proteins and their transient interactors. Protein-level enrichment for biotinylated proteins is well developed and popular, but direct detection of biotinylated proteins by peptide-level enrichment and the difference in results between direct and indirect detection remain underexplored. To address this gap, we compared and improved enrichment and data analysis methods using TurboID fused to SPY, a low-abundance O-fucose transferase, using an AAL-enriched SPY target library for cross-referencing. Our results showed that MyOne and M280 streptavidin beads significantly outperformed antibody beads for peptide-level enrichment, with M280 performing best. In addition, while a biotin concentration [≤] 50 {micro}M is recommended for protein-level enrichment in plants, higher biotin concentrations can be used for peptide-level enrichment, allowing us to improve detection and data quality. FragPipes MSFragger protein identification and quantification software outperformed Maxquant and Protein Prospector for SPY interactome enrichment due to its superior detection of biotinylated peptides. Our improved washing protocols for protein-level enrichment mitigated bead collapse issues, improving data quality, and reducing experimental time. We found that the two enrichment methods provided complementary results and identified a total of 160 SPY-TurboID-enriched interactors, including 60 previously identified in the AAL-enriched SPY target list and 100 additional novel interactors. SILIA quantitative proteomics comparing WT and spy-4 mutants showed that SPY affects the protein levels of some of the identified interactors, such as nucleoporin proteins. We expect that our improvement will extend beyond TurboID to benefit other PL systems and hold promise for broader applications in biological research.

molecular biology↗

bioRxiv2019

An atlas of infiltrated B-lymphocytes in breast cancer revealed by paired single-cell RNA-sequencing and antigen receptor profiling

While it has been well-recognized that T-cell mediated adaptive cellular immunity plays important roles in cancer immune response and tumor control, the roles of B lymphocytes in tumor development and therapy have only been proposed until recently, and are still mostly controversial. To gain mechanistic insights into the origin and dynamics of tumor infiltrated immune cells, especially B lymphocytes, we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer (TNBC) infiltrated immune cells and present a comprehensive atlas of infiltrated B-lymphocytes in TNBC, the most aggressive breast cancer subtype. We demonstrate that TNBC infiltrated B cells showed more mature and memory B cell characteristics, as well as high clonality and extensive IgH class switching recombination and somatic hypermutations. The B cell signatures based on single-cell RNA-seq results are significantly associated with improved survival for TNBC patients and provide better prognostication than classic single B cell markers (CD19 or CD20). Further dissection of the mechanisms regulating the functions and dynamic distribution of tumor infiltrated B cell populations will provide new clues for tumor immunotherapy.

immunology↗

bioRxiv2019

Proteomic studies of the Arabidopsis TRAPP complexes reveal conserved organization and a novel plant-specific component with a role in plant development

How the membrane trafficking system spatially organizes intracellular activities and intercellular signaling networks is not well understood in plants. The Transport Protein Particle (TRAPP) complexes are known to play key roles in selective delivery of membrane vesicles to various subcellular compartments in yeast and animals, but remain to be fully characterized in plants. Here we interrogate the TRAPP complexes in Arabidopsis using quantitative proteomic approaches. TRS33 is a component shared by all TRAPP complexes in yeast and animals, and the Arabidopsis AtTRS33 is essential for the subcellular dynamics of other TRAPP components. Affinity purification of AtTRS33 followed by quantitative mass spectrometry identified fourteen interacting proteins; these include not only thirteen homologs of all known TRAPP components in yeast and mammals but also a novel protein we named TRAPP-interacting plant protein (TRIPP), which is conserved in multi-cellular photosynthetic organisms. Proteomic and molecular analyses showed that TRIPP specifically associates with the TRAPPII complex in vivo and directly interacts with the TRAPPII-specific subunits but not the subunits shared with TRAPPIII. TRIPP co-localizes with a subset of TRS33 compartments, and its localization is disrupted in the trs33 mutant. Loss-of-function tripp mutation caused growth and reproductive development defects, including partial photomorphogenesis in the dark. Our study demonstrates that plants possess at least two distinct TRAPP complexes similar to metazoan, and identifies TRIPP as a novel plant-specific component of the TRAPPII complex with important functions in plant growth and development.

plant biology↗