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Qu, Q.

Publications and source records attributed to Qu, Q..

18 recordsLinked to original sources
bioRxiv2026

Valine Engages a Prefrontal mGluR5 Allosteric Site to Preserve Social Behavior

Branched-chain amino acid metabolism is linked to neurodevelopmental disorders, but whether a defined amino acid directly modulates cortical receptor signaling to control behavior is unknown. Here, we show that valine is uniquely required for sociability through medial prefrontal cortex (mPFC) circuitry. Partial dietary valine restriction, but not comparable leucine or isoleucine restriction, or mPFC-restricted acceleration of BCAA catabolism through Bckdk loss, disrupts social interaction, and local valine supplementation rescues behavior. LiP-SMap, surface plasmon resonance, cryo-EM, and mutagenesis identify metabotropic glutamate receptor 5 (mGluR5) as a direct valine target and reveal a valine-selective allosteric pocket distinct from the glutamate site. Valine is signaling-biased: it drives {beta}-arrestin-linked output yet has little standalone Gq efficacy, instead potentiating glutamate-evoked mGluR5 signaling to recruit endocannabinoid/CB1 feedback, gate inhibitory transmission, and preserve mPFC-dependent social behavior. Together, these findings identify valine as a diet-derived allosteric ligand that links amino acid availability to cortical circuit control of social behavior.

neuroscience↗
bioRxiv2026

Phagocytic activity of perivascular cell promotes CNS injury pathology

Injury, stroke, and neurological diseases cause persistent accumulation of cellular debris that deteriorates lesion microenvironment and impedes central nervous system (CNS) repair. Debris clearance in the injured CNS has long been attributed primarily to microglia and infiltrating macrophages. Here, we identify perivascular cells as previously unrecognized phagocytes that expand after injury and exhibit robust phagocytic activity. Perivascular cell phagocytosis is conserved across multiple mouse models of CNS injury and human stroke lesions. These cells exhibit key hallmarks of phagocytosis, including LC3-associated phagocytosis for efficient lysosomal degradation. Mechanistically, phosphatidylserine serves as the eat-me signal and Axl mediates myelin debris uptake. Myelin phagocytosis drives perivascular cell proliferation, fibrosis and lesion progression. Genetic deletion of Axl in perivascular cells or pharmacological inhibition with the FDA-approved Axl inhibitor Gilteritinib reduces pathology and improves functional recovery after spinal cord injury. Together, these findings establish Axl-dependent perivascular cell phagocytosis as a therapeutic target for CNS repair.

neuroscience↗
bioRxiv2026

Faf2/Ubx2 potentiates p97/Cdc48 segregase activity via functional priming and reinforcement of the UT3 domain in Ufd1

The AAA+ segregase p97/Cdc48 extracts poly-ubiquitinated proteins from entrenched cellular environments to maintain proteostasis. However, its functional capacity is not uniform; extracting substrates from dense assemblies like stress granules or membrane necessitates a fully potentiated state. Here, using precisely synthesized ubiquitinated substrates, we show that the Faf2/Ubx2 cofactor hyperactivates p97/Cdc48, lowering its minimal ubiquitin chain requirement and broadening linkage specificity. Cryo-EM analysis of the activated complex demonstrates that Faf2/Ubx2 potentiates p97/Cdc48 segregase activity by structurally remodeling the substrate recognition module (K48-diUbProx) and priming its engagement with the AAA+ motor (p97/Cdc48-Npl4). These coordinated actions establish a pump-unit architecture that drives efficient substrate processing. Our findings illuminate a conserved mechanism that unlocks the maximal capacity of p97/Cdc48 and provide a blueprint for therapeutically targeting its hyper-activated state in disease.

biochemistry↗
bioRxiv2025

Conformation-specific Antibody Deciphers K27-linked Ubiquitination in Chaperone-Mediated Proteostasis

Lysine 27 (K27)-linked polyubiquitination plays critical yet incompletely defined roles in proteostasis, innate immunity, and disease progression; however, investigations into this process have long been hindered by its extremely low abundance and the lack of conformation-specific enrichment tools. Herein, we describe the development of a long-sought conformation-specific antibody, K27-IgG, which can selectively recognize--among all ubiquitin chain types--the unique architecture of K27-linked polyubiquitin (K27-polyUb) characterized by a distinct buried K27-isopeptide bond, with high affinity (KD = 4.66 nM). This antibody was derived from synthetic antibodies initially generated via phage display, using chemically synthesized K27-linked diubiquitin (K27-diUb) as the antigen. High-resolution co-crystal structures uncovered the unique K27-diUb interface targeted by these sAbs. Subsequent reformatting of these sAbs into a full-length human immunoglobulin G (IgG) scaffold yielded K27-IgG, notably exhibiting markedly enhanced affinity without compromising selectivity. Using K27-IgG as a tool, we achieved sensitive detection and immunoprecipitation (IP) of endogenous K27-polyUb in cells, and delineated the intracellular interaction landscape of K27-polyUb through complementary proteomic approaches. Two key findings emerged: 1) The molecular chaperone DNAJB1 is a specific reader of K27-linked ubiquitin chains (but not other linkages) and that K27-polyUb chains themselves exhibit chaperone-like activity, suggesting a novel mechanism by which K27-polyUb regulates chaperone-mediated proteostasis; 2) The E2 enzyme UBE2Q1 assembles K27-diUb, identifying it as a potential writer for this ubiquitin chain topology. Collectively, this study establishes K27-IgG as a robust tool for deciphering the K27-linked ubiquitin code, thereby opening new avenues for investigating the biological functions of K27-linked polyubiquitination. HighlightsO_LIFirst K27-linkage conformation-specific antibody with nanomolar affinity overcomes a major barrier in the field. C_LIO_LIK27-IgG unlocks functional mapping of the K27 ubiquitin landscape under proteotoxic stress. C_LIO_LIMolecular chaperone DNAJB1 is a selective "reader" of K27-linked ubiquitin chains. C_LIO_LIK27 chains possess intrinsic chaperone activity, enabling protein refolding and suppressing aggregation. C_LIO_LIE2 enzyme UBE2Q1 is a "writer" that directly assembles K27-linked ubiquitin chains. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/695067v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@113b980org.highwire.dtl.DTLVardef@1f7c1a0org.highwire.dtl.DTLVardef@c91656org.highwire.dtl.DTLVardef@1d9a507_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗
bioRxiv2024

Mechanistic Insights into the Stimulation of the Histone H3K9 Methyltransferase Clr4 by Proximal H3K14 Ubiquitination

H3K9 methylation is an evolutionarily conserved hallmark of heterochromatin and plays crucial roles in chromosome segregation, genome stability, and gene expression regulation. Clr4 is the sole histone methyltransferase responsible for catalyzing H3K9 methylation in Schizosaccharomyces pombe. Clr4 K455/K472 automethylation and histone H3K14 ubiquitination (H3K14Ub) are vital activators of the catalytic activity of Clr4, ensuring appropriate heterochromatin deposition and preventing deleterious gene silencing. While the mechanism by which automethylation activates Clr4 was recently elucidated, the mechanism of the significantly pronounced stimulatory effect of H3K14Ub on Clr4 remains unclear. Here we determined the crystal structures of Clr4 bound to ubiquitinated and unmodified H3 peptides at resolutions of 2.60 [A] and 2.39 [A], respectively. Our structures reveal a synergistic mechanism underlying the stronger stimulatory effect by H3K14Ub compared to automethylation: site-specific ubiquitination constrained by the H3K14 linkage increases substrate affinity through multivalent interactions between ubiquitin and Clr4. Additionally, H3K14Ub facilitates the allosteric transition of Clr4 from an inactive apo conformation to a hyperactive "catalyzing state", accompanied by conformational changes in the C-SET-insertion (SI) region, complete release of the autoregulatory loop (ARL), and retraction of the {beta}9/10 loop. Finally, we propose a structural model for the Clr4 catalytic-regulatory cycle, depicting varying levels of conformational regulation mediated by automethylation and ubiquitination. This work provides structural insights into the interplay between different histone modifications and their collective impact on epigenetic regulation.

molecular biology↗
bioRxiv2023

Lithocholic acid targets TULP3 to activate sirtuins and AMPK to retard ageing

Lithocholic acid (LCA), accumulated in the body during calorie restriction (CR), can confer administered metazoans with the ability to activate AMP-activated protein kinase (AMPK) and retard ageing. However, how LCA is signalled to activate AMPK and elicit the biological effects is unclear. Here, we show that LCA can enhance sirtuins (SIRTs) to deacetylate and subsequently inhibit vacuolar H+-ATPase (v-ATPase), thereby triggering AMPK activation via the lysosomal glucose-sensing pathway. Through proteomic analysis of SIRT1-coimmunoprecipitated proteins, we identify and validate that TUB like protein 3 (TULP3) is a constitutive component of SIRTs. Surprisingly, we found that TULP3 is an LCA receptor, and that the LCA-bound TULP3 activates SIRTs. The activated SIRTs in turn deacetylate the V1E1 subunit of v-ATPase on K52, K99 and K191 residues. Muscle-specific expression of the 3KR mutant of V1E1, mimicking the deacetylated state, dominantly activates AMPK and rejuvenates muscles in aged mice. Moreover, LCA once administered also activates AMPK and extends lifespan and healthspan in nematodes and flies, depending on the TULP3 homologues tub-1 and ktub, respectively. Our study thus elucidates that LCA triggers the TULP3-sirtuin-v-ATPase- AMPK route to manifest benefits of calorie restriction.

physiology↗
bioRxiv2023

Lithocholic acid phenocopies rejuvenating and life-extending effects of calorie restriction

Calorie restriction (CR) is a dietary intervention to promote health and longevity. CR causes various metabolic changes in both the production and circulation of metabolites; however, it remains unclear which of the changed metabolite(s) can account for the physiological benefits of CR. Through metabolomic analysis of metabolites undergoing abundance changes during CR and subsequent functional validation, we found that lithocholic acid (LCA) is the only metabolite that alone can recapitulate the effects of CR, including activation of AMPK and the rejuvenating effects of muscle regeneration, grip strength and running capacity in mice. Interestingly, LCA also activates AMPK and exerts life- and health-extending effects in Caenorhabditis elegans and Drosophila melanogaster, indicating that these animal models are able to transmit the signalling of LCA once administered. Knockout of AMPK abrogates LCA-induced phenotypes, in nematodes and flies, as well as in mice. Together, we have identified that administration of the CR-upregulated metabolite LCA alone can confer anti-ageing benefits to metazoans, in an AMPK-dependent manner.

physiology↗
bioRxiv2023

Transport and inhibition mechanism for VMAT2-mediated synaptic loading of monoamines

Monoamine neurotransmitters such as serotonin and dopamine are loaded by vesicular monoamine transporter 2 (VMAT2) into synaptic vesicles for storage and subsequent release in neurons. Impaired VMAT2 function underlies various neuropsychiatric diseases. VMAT2 inhibitors reserpine and tetrabenazine are used to treat hypertension, movement disorders associated with Huntingtons Disease and Tardive Dyskinesia. Despite its physiological and pharmacological significance, the structural basis underlying substrate recognition, and inhibition by varying mechanisms remains unknown. Here we present cryo-EM structures of human apo VMAT2 in addition to states bound to serotonin, tetrabenazine, and reserpine. These structures collectively capture three states, namely the lumen-facing, occluded, and cytosol-facing conformations. Notably, tetrabenazine induces a substantial rearrangement of TM2 and TM7, extending beyond the typical rocker-switch movement. These functionally dynamic snapshots, complemented by biochemical analysis, unveil the essential components responsible for ligand recognition, elucidate the proton-driven exchange cycle, and provide a framework to design improved pharmaceutics targeting VMAT2.

biophysics↗
bioRxiv2023

Evolution of the enhancer-rich regulatory region of the POU1F1 gene.

Precise spatio-temporal expression of genes in organogenesis is regulated by the coordinated interplay of DNA elements such as promoter and enhancers present in the regulatory region of a given locus. POU1F1 transcription factor plays a crucial role in the development of somatotrophs, lactotrophs and thyrotrophs in the anterior pituitary gland, and in maintaining high expression of growth hormone, prolactin and TSH. In mouse, expression of POU1F1 is controlled by a region fenced by two CTCF sites, containing 5 upstream enhancer elements, designated E-A (5 to 3). We performed comparative sequence analysis of this regulatory region and discovered that three elements, B, C and E, are present in all vertebrate groups except Agnatha. One very long (>2kb) element (A) is unique to mammals suggesting a specific change in regulation of the gene in this group. Using DNA accessibility assay (ATAC-seq) we showed that conserved elements in anterior pituitary of four non-mammals are open, suggesting functionality as regulatory elements. We showed that, in many non-mammalian vertebrates, an additional upstream exon closely follows element E, leading to alternatively spliced transcripts. Here, element E functions as an alternative promoter, but in mammals this feature is lost, suggesting that conversion of alternative promoter to enhancer could be one evolutionary mechanism for enhancer birth. Our work shows that regulation of POU1F1 changed markedly during the course of vertebrate evolution, use of a small number of enhancer elements combined with alternative promoters in non-mammalian vertebrates being replaced by use of a unique combination of enhancers in mammals.

evolutionary biology↗
bioRxiv2023

AMPK targets PDZD8 to trigger carbon source shift to glutamine

The shift of carbon utilisation from glucose to other nutrients is a fundamental metabolic adaptation to cope with the decreased glucose oxidation during fasting or starvation1. AMP-activated protein kinase (AMPK) plays crucial roles in manifesting physiological benefits accompanying glucose starvation or calorie restriction2. However, the underlying mechanisms are unclear. Here, we show that low glucose-induced activation of AMPK plays a decisive role in the shift of carbon utilisation from glucose to glutamine. We demonstrate that endoplasmic reticulum (ER)-localised PDZD8, which we identify to be a new substrate of AMPK, is required for the glucose starvation-promoted glutaminolysis. AMPK phosphorylates PDZD8 at threonine 527 (T527), and promotes it to interact with and activate the mitochondrial glutaminase 1 (GLS1), a rate-limiting enzyme of glutaminolysis3-5, and as a result the ER-mitochondria contact is strengthened. In vivo, PDZD8 enhances glutaminolysis, and triggers mitohormesis that is required for extension of lifespan and healthspan in Caenorhabditis elegans subjected to glucose starvation or caloric restriction. Muscle-specific re-introduction of wildtype PDZD8, but not the AMPK-unphosphorylable PDZD8-T527A mutant, to PDZD8-/- mice is able to rescue the increase of glutaminolysis, and the rejuvenating effects of caloric restriction in aged mice, including grip strength and running capacity. Together, these findings reveal an AMPK-PDZD8-GLS1 axis that promotes glutaminolysis and executes the anti-ageing effects of calorie restriction by promoting inter-organelle crosstalk between ER and mitochondria.

cell biology↗
bioRxiv2023

Evolution of the gene regulatory network of body axis by enhancer hijacking in amphioxus

A central goal of evolutionary developmental biology is to decipher the evolutionary pattern of gene regulatory networks (GRNs) that control morphogenesis during embryonic development, and the underlying molecular mechanism of the GRNs evolution. The Nodal signaling that governs the body axes of deuterostomes exhibits a conserved GRN orchestrated principally by Nodal, Gdf1/3 and Lefty. Despite that the GRN retains a conserved function in deuterostomes, the expression patterns of Gdf1/3 and Nodal are derived in cephalochordate amphioxus, implying a specific rewiring of the GRN in this lineage. Here we examined the regulatory mechanism and evolution of this GRN in amphioxus by functional genetic manipulations. We found that while the amphioxus Gdf1/3 orthologue shows nearly no expression during embryogenesis, its duplicate Gdf1/3-like linking to Lefty is zygotically expressed in a similar pattern as Lefty. Mutant and transgenic analyses revealed that Gdf1/3 is no longer crucial for amphioxus axial development. Instead, Gdf1/3-like assumes this responsibility, likely through hijacking Lefty enhancers. We also showed that amphioxus Nodal has become an indispensable maternal factor to compensate for the loss of maternal Gdf1/3 expression. We therefore demonstrated a case that the evolution of an ancestral GRN could be triggered by enhancer hijacking events. This pivotal event has allowed the emergence of a new GRN in the extant amphioxus, presumably evolving through a stepwise process. The co-expression of Gdf1/3-like and Lefty achieved by shared regulatory region may have provided developmental robustness during body axis formation in extant amphioxus, which provides a selection-based hypothesis for the phenomena called developmental system drift.

evolutionary biology↗
bioRxiv2023

Opposing implications of co-evolutionary lineages and traits of gut microbiome on human health status

Little is known about the co-evolutionary history of the human gut microbe and its relevance to host physiology. Here, we constructed a gut prokaryotic genomic database of wild primates (pSGBs) and compared it with the human gut prokaryotic database (hSGBs) to define shared co-evolutionary clusters (SCEC-hSGBs) and co-evolutionary traits of hSGBs. We analyzed the evolutionary trends of specific functions like carbohydrate-active enzymes and antibiotic resistance in hSGBs and uncovered host-jumping events and genome reduction tendencies in SCEC-hSGBs. Intriguingly, the SCEC-hSGBs and the super enrichers of the traits (SUEN-hSGBs), which are putatively partially derived from carnivores, showed opposite implications for host health status. Specifically, SUEN-hSGBs are enriched in various diseases, showing a negative correlation with gut biodiversity and disproportionate contributions to the known health-negative marker taxa and metabolite. Our study provides insight into the origin and adaptability of human gut microbes and references for developing probiotics and microbiome-based host health prediction.

microbiology↗
bioRxiv2022

Structure-based Evolution of G protein-biased μ-opioid Receptor Agonists

The -opioid receptor (OR) is the major target for opioid analgesics. Activation of OR initiates signaling through G protein pathways as well as through {beta}-arrestin recruitment. OR agonists that are biased towards G protein signaling pathways demonstrate diminished side effects. PZM21, discovered by computational docking, is a G protein biased OR agonist. Here we report the cryoEM structure of PZM21 bound OR in complex with Gi protein. Structure-based evolution led to multiple PZM21 analogs with more pronounced Gi protein bias and increased lipophilicity to improve CNS penetration. Among them, FH210 shows extremely low potency and efficacy for arrestin recruitment. We further determined the cryoEM structure of FH210 bound to OR in complex with Gi protein and confirmed its expected binding pose. The structural and pharmacological studies reveal a potential mechanism to reduce {beta}-arrestin recruitment by the OR, and hold promise for developing next-generation analgesics with fewer adverse effects. Table of Contents Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=43 SRC="FIGDIR/small/485330v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@125808corg.highwire.dtl.DTLVardef@11aa15corg.highwire.dtl.DTLVardef@157caaaorg.highwire.dtl.DTLVardef@ba837d_HPS_FORMAT_FIGEXP M_FIG C_FIG We obtained cryoEM structures of the -opioid receptor (OR) bound to the lead compound PZM21 and the newly developed agonist FH210 to understand the mechanism of their biased signaling and to guide the evolution of next-generation analgesics with fewer adverse effects.

pharmacology and toxicology↗
bioRxiv2021

Replication is the key barrier during the dual-host adaption of mosquito-borne flaviviruses

Mosquito-borne flaviviruses (MBFs) adapt to a dual-host transmission circle between mosquitoes and vertebrates. Dual-host affiliated insect-specific flaviviruses (dISFs), discovered from mosquitoes, are phylogenetically similar to MBFs but do not infect vertebrates. Thus, dISF-MBF chimeras could be an ideal model to study the dual-host adaption of MBFs. Using the pseudo-infectious reporter virus particle and reverse genetics systems, we found dISFs entered vertebrate cells as efficiently as the MBFs, but failed to initiate replication. Exchange of the un-translational regions (UTRs) of Donggang virus (DONV), an dISF, with those from Zika virus (ZIKV) rescued DONV replication in vertebrate cells and critical secondary RNA structures were further mapped. Essential UTR-binding host factors were screened for ZIKV replication in vertebrate cells, displaying different binding patterns. Therefore, our data demonstrate a post-entry cross-species transmission mechanism of MBFs, while UTR-host interaction is critical for dual-host adaption. Significance StatementMost viruses have a relatively narrow host range. In contrast, vector-borne flaviviruses, such as dengue virus and Zika virus, maintain their transmission cycle between arthropods and vertebrates, belonging to different phyla. How do these viruses adapt to the distinct cellular environments of two phyla? By comparing the single-host insect specific flavivirus and dual-host Zika virus, we identified three key molecular factors that determine MBF host tropism. This study will greatly increase the understanding of entry, replication, and cross-species evolution of mosquito-borne flaviviruses.

microbiology↗
bioRxiv2021

Structural insights into distinct signaling profiles of the μOR activated by diverse agonists

Drugs targeting the G protein-coupled -opioid receptor (OR) are the most effective analgesics available but are also associated with fatal respiratory depression. While some partial opioid agonists appear to be safer than full agonists, the signaling pathways responsible for respiratory depression have yet to be elucidated. Here we investigated the structural and mechanistic basis of action of lofentanil (LFT) and mitragynine pseudoindoxyl (MP), two OR agonists with different safety profiles. LFT, one of the most potent and lethal opioids, and MP, a derivative from the kratom plant with reduced respiratory depression in animal studies at equianalgesic doses, exhibited markedly different signaling efficacy profiles for G protein subtype activation and recruitment of {beta}-arrestins. Cryo-EM structures of the OR-Gi1 complex with MP (2.5[A]) and LFT (3.2[A]) revealed that the two ligands engage distinct sub-pockets, and molecular dynamics (MD) simulations showed additional differences in the binding site that propagate to the intracellular side of the receptor where G proteins and {beta}-arrestins bind. While MP favors the precise G protein-bound active state observed in the cryo-EM structures, LFT favors a distinct active state. These results highlight how drugs engaging different parts of the OR orthosteric pocket can lead to distinct signaling outcomes.

biophysics↗
bioRxiv2020

Expression analysis of photosynthesis-related genes in albino Artocarpus heterophyllus seedlings leaves

Albino Artocarpus heterophyllus Seedlings (AAS) were found in the preliminary investigation by our group and were used as materials for researching. The phenotype of AAS leaves were observed and measured. In parallel, the photosynthetic physiological parameters were determined under different photosynthetically active radiations (PAR). The results suggested that the length, width, area and thickness of AAS leaves were less than normal seedings. Likewise, the net photosynthetic rate, intercellular CO2 concentration, stomatal conductance and transpiration rate of AAS leaves were not susceptible to PAR in contrast to normal individuals. Furthermore, the transcriptome sequencing technology was performed to clarify the expression of genes related to photosynthesis. It is as expected that numerous down-regulated genes were found in the synthesis of photosynthetic pigments, as well as the pathways of photosynthesis - antenna proteins, photoreaction and carbon fixation reaction of AAS leaves. Compared to other albino plants, AAS have a longer life span and more stable phenotypic traits with larger leaves, which could provide ideal materials for investigating photosynthesis of woody plants.

physiology↗
bioRxiv2020

Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+ channels in nanodisc

NaChBac, the first bacterial voltage-gated Na+ (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Nav channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the cryo-EM analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav channels in lipid bilayers. To study GMTs in mammalian Navs, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaces the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 [A] and 3.2 [A] resolutions, respectively. Compared to the structure of HWTX-IV-bound human Nav1.7, which was obtained at an overall resolution of 3.2 [A], the local resolution of the toxin has been improved from ~ 6 [A] to ~ 4 [A]. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav channels in a membrane environment.

biophysics↗