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Lang, X.

Publications and source records attributed to Lang, X..

12 recordsLinked to original sources

Platycodin D2 Targets Vimentin to Suppress Fibroblast-Myofibroblast Transition: A Novel Therapeutic Strategy Against Pulmonary Fibrosis

Background Pulmonary fibrosis is a progressive lung disease characterized by excessive extracellular matrix deposition and irreversible decline in lung function with limited effective therapeutic targets. Vimentin, a type III intermediate filament protein, plays a critical role in fibroblast activation and fibrogenesis, representing a promising drug target. Methods Novel vimentin ligands were screened via virtual screening. SPR assay verified compound-vimentin binding affinity. CETSA and CD spectroscopy analyzed protein structural changes after compound binding. In vitro FMT model and in vivo bleomycin-induced pulmonary fibrosis model were used to assess antifibrotic effects, and mutagenesis assays identified key binding amino acid residues. Results Platycodin D2 (PD2) from Platycodon grandiflorus was identified as a novel high-affinity vimentin ligand (Kd = 392.8 nM). PD2 binds vimentin directly, alters its secondary structure and induces insoluble aggregation. It effectively inhibits TGF-{beta}1-induced FMT in vitro and mitigates bleomycin-induced pulmonary fibrosis in vivo, reducing collagen deposition and improving animal survival. Critically, mutagenesis validation confirmed that key residues (Glu138 in chain A, Glu132 and Glu143 in chain B, as well as Glu50 and Arg54 in chain C) are essential for this interaction. Conclusions Our findings establish PD2 as a novel pharmacological inducer of aberrant vimentin aggregation, presenting a distinct target-driven strategy for antifibrotic drug development.

cell biology↗

Isolation of functional endogenous clathrin-coated vesicles and in vitro reconstitution of pure clathrin cages

Clathrin-coated vesicles (CCVs) mediate key endocytic trafficking events, and dysfunction of CCVs is linked to multiple human diseases. Conventional centrifugation-based purification protocols can enrich endogenous CCVs but fail to eliminate intraluminal smooth vesicles (SVs) and co-isolated exosomes; these lipid contaminants reduce sample homogeneity and hinder high-resolution structural and proteomic analysis. Here, we present an integrated workflow to isolate biologically active endogenous CCVs from porcine brain and reconstitute homogeneous, SV-free clathrin cages. Crude CCVs are first enriched by differential and sucrose density gradient centrifugation to deplete the majority of exosomes. Clathrin cages are then depolymerized under alkaline conditions, allowing separation of soluble clathrin and adaptor proteins from SVs and residual lipid contaminants via ultracentrifugation. Purified coat proteins are reassembled in vitro into uniform clathrin cages. Functional assays confirm that purified CCVs retain Auxilin-Hsc70-dependent uncoating activity, and the enclosed SVs carry active vATPase proton pumps. This approach produces well-defined samples suitable for cryo-electron microscopy and mass spectrometry-based investigation of clathrin assembly and disassembly.

biochemistry↗

Repurposing of the assembly chaperone PAC1-PAC2 defines a specialized proteasome landscape in mature mammalian sperm

Mature mammalian sperm rely on active proteasomes containing the testis-specific subunit 4s for capacitation, acrosomal exocytosis and fertilization, but how these proteasomes are structurally specialized remains unclear. We determine the endogenous proteasome landscape of mature bovine spermatozoa and testis using cryo-electron microscopy. We resolve five sperm proteasome assemblies: PA200-20S, free 20S, a previously unrecognized PA200-20S-PAC1/2 hybrid, and PAC1/2-20S complexes capped at one or both ends. Unexpectedly, the PAC1/2-bound complexes are mature and POMP-free, selectively incorporated for 4s, lack 2, and adopt a PAC1/2 orientation and gate configuration distinct from known assembly intermediates. Together with elevated proteolytic activity, these features indicate that PAC1/2 is repurposed from a transient assembly chaperone into a stable post-assembly regulator in mature sperm. 4s-containing proteasomes assemble through the canonical PAC1-PAC4/POMP pathway yet may follow {beta}2-{beta}3-{beta}1 incorporation ordering; functionally, 4s incorporation remodels the sCP surface and enhances peptidase activities, definining the spermatoproteasomes as a hyperactive 20S variant. PAC1/2-bound proteasomes are absent from testis, where PA200-20S and 26S proteasomes are present, while 26S proteasomes are nearly lost in mature sperm. Our findings define a sperm-specific, ATP-independent proteasome landscape, expand the functional repertoires of 4s and PAC1/2, and provide a structural framework for proteasome specialization in male fertility.

cell biology↗

Cell membrane proteome profiling uncovers molecular signatures and GPCR regulators underlying diet-induced obesity and exercise-mediated adaptation

Cell membrane proteins (CMPs), notably G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs), represent the largest class of druggable targets. Despite their therapeutic importance, how the CMP landscape is systemically remodeled during metabolic disease progression and in response to exercise remains poorly understood. Here, we constructed the most comprehensive CMP proteome atlas to date across 22 male mouse tissues and established the first multi-tissue map of GPCR-associated protein hormones/prohormones. Integrated CMP proteomic and transcriptomic analysis revealed that diet-induced obesity and its progression to type 2 diabetes remodel the CMP repertoire in patterns distinct from those induced by exercise. We found that numerous GPCRs and RTKs critical for energy homeostasis are dysregulated during obesity in a tissue-specific manner, and these alterations are reversed to varying extents by exercise training. Importantly, our CMP-centric omics study identified two parathyroid hormone receptors (PTHRs) in the hypothalamus as negative regulators of feeding and body weight. Genetically silencing these hypothalamic PTHRs led to severe obesity even on a chow diet and markedly blunted exercise-induced weight loss. Collectively, our study provides not only new insights into systematic CMP regulation underlying metabolic deterioration versus exercise adaptation, but also nominates potential receptor targets for obesity management.

biochemistry↗

A dual-factor complex governs archaeal ribosome hibernation by sensing energy status

Efficient coupling of cellular energy status to ribosome regulation is fundamental for cellular survival. Here, we identify the Archaeal Ribosome regulatory Complex (ARC)--a previously uncharacterized dual-factor complex comprising ARC-P and ARC-A. Cryo-EM reveals that ARC anchors to the small ribosomal subunit, establishing a stringent blockade of the tRNA and mRNA paths via an electrostatic wedge mechanism. This hibernation state is modulated by energy status: the complex remains stably associated under low-energy conditions, whereas ATP binding triggers rapid mobilization. Genetic analyses demonstrate that ARC acts as a translational brake essential for preserving ribosomal structural integrity, with ARC-A serving as the primary inhibitory factor. Notably, while the loss of ARC accelerates growth, it impairs recovery in proportion to stress severity. Phylogenomic analysis identifies ARC as an evolutionarily novel and widely distributed dual-factor system, revealing a conserved regulatory strategy for metabolic-translational coupling across diverse archaea. Our findings define a fundamental strategy where modular complexes integrate metabolic sensing with mechanical sequestration to balance growth and persistence.

biochemistry↗

Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming

The therapeutic promise of tumor microbial peptides faces a critical safety paradox: tumors and peritumor tissues harbor compositionally similar microbiomes, yet safe immunotherapy demands tumor-specific targeting. We performed comprehensive transcriptomic analysis of microbial communities from 1,868 tumor and peritumor samples across 11 cancer types. Although 88.5% of microbial species are present in both tissue types, tumor and peritumor tissues exhibit profound transcriptional divergence: only 34.1% of microbial genes are expressed in both tissue types, and merely 18.2% of predicted HLA-binding peptides overlap. This transcriptional divergence represents microbial transcriptional reprogramming (MTR) in tumor tissues, through which microbes activate distinct genomic regions while adapting to tumor microenvironmental pressures, thereby generating tumor-specific peptide repertoires. Using Microbial Transcriptional Reprogramming Index (MiTRI) to quantify MTR, we found that higher MiTRI values correlate with expanded immunogenic peptide repertoires. Mass spectrometry-based immunopeptidomics confirmed that 25% of naturally presented microbial peptides originate from MTR regions. Crucially, in microsatellite-stable colorectal cancer, neo-adjuvant therapy responders exhibited significantly higher MiTRI values. T cell receptors (TCRs) recognized MTR-derived epitopes at 2.10-fold higher rates than genome-wide epitopes, accounting for 79.1% of clonally expanded TCRs. These findings establish MTR as the principle that ensures the tumor-specificity and safety of micorbiome-directed immunotherapy.

cancer biology↗

A simplified and highly efficient cell-free protein synthesis system for prokaryotes

Cell-free protein synthesis (CFPS) systems are a powerful platform with immense potential in fundamental research, biotechnology, and synthetic biology. Conventional prokaryotic CFPS systems, particularly those derived from Escherichia coli (E. coli), often rely on complex reaction buffers containing up to thirty-five components, limiting their widespread adoption and systematic optimization. Here, we present an optimized E. coli cell-free protein synthesis (eCFPS) system, which is significantly streamlined for high efficiency. Through systematic screening, we successfully reduced the essential core reaction components from 35 to a core set of 7. The thorough optimization of these seven key components ensured that protein expression levels were not only maintained but even substantially improved. Furthermore, we developed a much simpler procedure for preparing the bacterial cytosolic extracts, a "fast lysate" protocol that eliminates the traditional time-consuming runoff and dialysis steps, thereby enhancing the overall accessibility and robustness of eCFPS. This optimized and user-friendly eCFPS efficiently synthesizes challenging proteins, including functional, self-assembling vimentin, and active restriction endonuclease BsaI despite its strong cytotoxicity, and serves as a powerful tool that will facilitate diverse applications in basic life science research and beyond.

biochemistry↗

{Psi}-Atlas: an integrated atlas for pseudouridine epitranscriptome

Pseudouridine ({Psi}) is a C5 glycoside isomer of uridine, formed by breaking the N1 glycosyl bond and undergoing a 180{degrees} base rotation. This modification stands as one of the most widespread post-transcriptional alterations in RNA and is universally distributed among diverse RNA species. The pervasiveness of this modification enhances RNA structural integrity, bestows unique structural and functional attributes upon the RNA molecules it adorns, and facilitates additional hydrogen bonding. However, the absence of a convenient and integrated intuitive visualization database encompassing all currently reported species and RNA types is evident. Here, we present the {Psi}-Atlas, an extensive database meticulously curated for the comprehensive collection and annotation of RNA pseudouridine. This database encompasses 554,895 pseudouridine modification sites across various RNA categories, including mRNA, ncRNA, tRNA, rRNA, and others, in 55 distinct species reported in current literature. The sequencing methodologies employed comprise the next-generation sequencing (NGS) techniques such as {Psi}-Seq, Pseudo-Seq, CeU-Seq, PSI-Seq, RBS-Seq, HydraPsiSeq, BID-Seq, PRAISE-Seq, as well as third-generation sequencing methods like Direct RNA sequencing (DRS). {Psi}-Atlas as the most comprehensive and integrated resource for RNA pseudouridine modifications to date. And the {Psi}-Atlas database offers an intuitive interface for information display and a myriad of analytical tools, including PsiVar and PsiFinder. In essence, this platform serves as a robust search and visualization tool for the study of pseudouridylation in epitranscriptomics. {Psi}-Atlas is available at https://rnainformatics.org.cn/PsiAtlas.

bioinformatics↗

Geminivirus C4 proteins inhibit GA signaling via prevention of NbGAI degradation, to promote viral infection and symptom development in N. benthamiana

Phytohormone gibberellin (GA) is an important plant signaling molecule that regulates plant growth and defense against abiotic and biotic stresses. To date, the molecular mechanism of the plant responses to viral infection mediated by GA is still undetermined. DELLA is a repressor of GA signaling and is recognized by the F-box protein, a component of the SCFSLY1/GID2 complex. The recognized DELLA is degraded by the ubiquitin-26S proteasome, leading to the activation of the GA signaling. Here, we report that ageratum leaf curl Sichuan virus (ALCScV)-infected N. benthamiana plants showed dwarfing symptom and abnormal flower development. The infection of ALCScV alters the expressions of GA pathway-related genes and decreases the content of endogenous GA significantly in N. benthamiana. Further, ALCScV-encoded C4 protein interacts with the DELLA protein NbGAI, and interferes with the interaction between NbGAI and NbGID2 to prevent the degradation of NbGAI, leading to the inhibition of the GA signaling pathway. Silencing of NbGAI or exogenous GA3 treatment significantly reduces viral accumulation and disease symptoms in N. benthamiana plants. The same results were proved by the experiments with C4 protein encoded by tobacco curly shoot virus (TbCSV). Therefore, we propose a novel mechanism of geminivirus C4 proteins controling virus infection and disease symptom development through interfering GA signaling pathway. Author SummaryGibberellins (GAs) are plant hormones that are essential for many developmental processes in plants. It has indicated that plant virus infection can induce abnormal flower development and influence GA pathway resulting the plant dwarfing symptom, but the underlying mechanisms is still not well described. Here, we demonstrate that geminivirus - encoded C4 protein regulates the GA signaling pathway to promote viral accumulation and disease symptom development. Through directly interacting with NbGAI, the C4 protein interferes with the interaction between NbGAI and NbGID2, which inhibits the degradation of NbGAI. As a result, the GA signaling pathway is blocked, and the infected plants display symptoms of typical dwarfing and delayed flowering. Our results reveal a novel mechanism by which geminivirus C4 proteins influence viral pathogenicity via interfering the GA signaling pathway, and provide new insights into the interaction between virus and host.

pathology↗

Recombinant Fc-fusion vaccine of RBD induced protection against SARS-CoV-2 in non-human primate and mice

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to infect people globally. The increased COVID-19 cases and no licensed vaccines highlight the need to develop safe and effective vaccines against SARS-CoV-2 infection. Multiple vaccines candidates are under pre-clinical or clinical trails with different strengths and weaknesses. Here we developed a pilot scale production of a recombinant subunit vaccine (RBD-Fc Vacc) with the Receptor Binding Domain of SARS-CoV-2 S protein fused with the Fc domain of human IgG1. RBD-Fc Vacc induced SARS-CoV-2 specific neutralizing antibodies in non-human primates and human ACE2 transgenic mice. The antibodies induced in macaca fascicularis neutralized three divergent SARS-CoV2 strains, suggesting a broader neutralizing ability. Three times immunizations protected Macaca fascicularis (20ug or 40ug per dose) and mice (10ug or 20ug per dose) from SARS-CoV-2 infection respectively. These data support clinical development of SARS-CoV-2 vaccines for humans. RBD-Fc Vacc is currently being assessed in randomized controlled phase 1/II human clinical trails. SummaryThis study confirms protective efficacy of a SARS-CoV-2 RBD-Fc subunit vaccine.

immunology↗

Azetidines kill Mycobacterium tuberculosis without detectable resistance by blocking mycolate assembly.

Tuberculosis (TB) is the leading cause of global morbidity and mortality resulting from infectious disease, with over 10 million new cases and 1.5 million deaths in 2019. This global emergency is exacerbated by the emergence of multi-drug-resistant MDR-TB and extensively-drug-resistant XDR-TB, therefore new drugs and new drug targets are urgently required. From a whole-cell phenotypic screen a series of azetidines derivatives termed BGAz, that elicit potent bactericidal activity with MIC99 values <10 M against drug-sensitive Mycobacterium tuberculosis and MDR-TB were identified. These compounds demonstrate no detectable drug resistance. Mode of action and target deconvolution studies suggest that these compounds inhibit mycobacterial growth by interfering with cell envelope biogenesis, specifically late-stage mycolic acid biosynthesis. Transcriptomic analysis demonstrates that the BGAz compounds tested display a mode of action distinct from existing mycobacterial cell-wall inhibitors. In addition, the compounds tested exhibit toxicological and PK/PD profiles that pave the way for their development as anti-tubercular chemotherapies.

microbiology↗

The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species

Magnolia biondii Pamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Contributing a genome sequence for M. biondii will help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution in Magnolia. We assembled a chromosome-level reference genome of M. biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was 2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete gene ratio of 91.90%. About 89.17% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 48,319 protein-coding genes, accounting for 22.97% of the genome length, in contrast to 66.48% of the genome length for the repetitive elements. We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae. Functional enrichment of the Magnolia specific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage. Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of M. biondii could empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms.

plant biology↗