Biology subjects

Zhang, C.

Publications and source records attributed to Zhang, C..

At least 271 records · Page 15Linked to original sources

bioRxiv2025

Mechanistic Insight of Tardigrade Anhydrobiosis via Protein Structural Analysis

Tardigrades are microscopic organisms with extraordinary tolerance to environmental stresses such as desiccation and thus offer unique solutions to bio-preservation, anti-aging, and interstellar travel. Recent studies revealed a collection of cytoplasmic and secretory abundant soluble proteins (CAHSs and SAHSs respectively) contributing to tardigrades extreme resilience. Using computational tools, I examined 39 CAHSs and 28 SAHSs from three representative tardigrade species. Both protein families possess a conserved central region and two highly variable terminal regions. Phylogenetic analysis suggests that CAHSs and SAHSs have distinct sequences despite functional similarity. AlphaFold predicts that CAHSs central region forms a long and amphiphilic -helix whereas SAHSs folds into {beta}-barrel. Since dehydration leads to the increase of intracellular protein concentration, I used AlphaFold to simulate CAHS oligomerization and find that they preferably dimerize via their central helix motifs. Examination of CAHS dimers reveals a strong inter-helix interaction. The dimerized anti-parallel helix bundle has hydrophobic and hydrophilic sides, resembling lipid-interacting proteins like ApoE. Empirical tests using mammalian fibroblast cells expressing the representative RvCAHS3 show that CAHSs concentrated on intracellular membranes instead of in proteinaceous condensates during dehydration. Moreover, RvCAHS3 significantly improves cell survival as measured by the stimulation-evoked release of Ca2+ from membrane-enclosed internal stores like endoplasmic reticulum. Taken together, these results suggest that CAHS inclines to dimerize and further forms a mesh on intracellular membranes to reinforce them during environmental stresses. By so doing, CAHSs can protect the integrity and the functionality of membrane-enclosed organelles. This finding implicates new strategies to preserve biomolecules, cells, and tissues under challenging conditions or for easy transportation.

biophysics↗

bioRxiv2025

DICAR-JP Regulates Ribosome Migration, a New Theory of Mitochondrial Protein Production

BackgroundDICAR plays a cardioprotection of diabetic models. DICAR-JP, a short sequence of DICAR, may represent DICARs active functional domain. NAC is necessary for the heart tissue development. Addtionally, OGDHL is a metabolism regulator. In this study, we examine a new mechanism of DICAR via NAC/OGDHL on regulating cardiomyocyte metabolism in DCM. We also sought to elucidate the function of DICAR/DICAR-JP in modulating NAC-dependent production of OGDHL nascent peptides and their mitochondrial translocation, and we also aimed to optimize the DICAR-JP sequence to be better therapy on DCM. MethodsSPR was to investigate the binding interaction between DICAR-JP and NAC. The function of DICAR-JP and DICAR-JP45 on OGDHL nascent peptide transfection was detected by in vitro translation approach. Biotin-DICAR-JP was transfected to study the function of DICAR-JP, NAC and OGDHL. Untargeted metabolomics was utilized to characterize the metabolic reprogramming of cardiomyocytes. AAV9-DICAR-JP and DICAR-JP45 were constructed and administered to db/db mice for 1-2 months to assess their cardioprotective effects detected by Echocardiography confirmed mouse cardiac function. ResultsOur findings demonstrated that DICAR-JP be the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. Disruption of OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP facilitated the translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria, leading us to hypothesize that DICAR-JP plays a key role in regulating ribosomal migration from the endoplasmic reticulum to the mitochondria. We refer to this process as the Ribosome Migration. In our studies using AAV9-mediated DICAR-JP and DICAR-JP45 overexpression in heart tissue. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Empagliflozin. ConclusionsIn a conclusion, we propose a new endogenous nucleic acid candidate drug library, and a new molecular framework, the Ribosome Migration, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. This theory constructs a new mitochondrion protein from nuclear original protein. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSDICAR is a new protective circular noncoding RNA for diabetic cardiomyopathy. NAC is located in ribosome and regulates new peptide production, which is also a key factor in heart tissue development. OGDHL can regulate different energy metabolism in mitochondria. What New Information Does This Article Contribute?DICAR-JP is the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. There is an interaction between DICAR-JP and NAC. DICAR-JP sequence is protected by NAC and NAC function is mediated by DICAR-JP. We called this RNA functional domain. OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP takes part in tanscription and translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria via plasma ribosome. We call this process the Ribosome Migration Theory. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Dapagliflozin (DAPA). Our study revealed a novel molecular framework, the Ribosome Migration Theory, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM.

pharmacology and toxicology↗

bioRxiv2025

Single-Cell eQTL Mapping Reveals Cell Type-Specific Genetic Regulation in Lung Cancer

Genome-wide association studies (GWAS) have identified over 50 lung cancer risk loci; however, the precise cellular context of these genetic mechanisms remains unclear due to limitations in bulk tissue eQTL analyses. Here, we present the largest single-cell eQTL atlas of human lung tissue to date, profiling 222 donors using multiplexed scRNA-seq. We identified 16,785 eQTLs across 17 cell types, with over 90% of sc-eQTLs and 59% eGene being cell-type-specific, and fewer than 23% were detectable in paired bulk datasets. Integration with GWAS for non-small cell lung cancer highlighted epithelial and immune cells as key contributors to genetic susceptibility, identifying 28 candidate genes within known risk loci and 24 in novel regions. Notably, 47% of established NSCLC susceptibility loci exhibited cell-type-specific pleiotropic genetic regulation. This study provides a valuable resource of lung sc-eQTLs and illuminates how genetic variation modulates gene expression in a cell-type-specific fashion, contributing to lung cancer susceptibility.

genetics↗

bioRxiv2025

Structural and Functional Studies of Rabbit SAMD9 Reveal a Distinct tRNase Module That Underlies the Antiviral Activity

Human SAMD9 and SAMD9L (collectively SAMD9/9L) are large cytoplasmic proteins with antiviral and antiproliferative activities, recently shown to regulate protein synthesis by specifically cleaving phenylalanine tRNA (tRNAPhe). The enzymatic activity of human SAMD9 (hSAMD9) resides within its N-terminal tRNase domain, which depends on three essential basic residues for tRNA binding and biological activity. While these residues are highly conserved across mammalian SAMD9/9L, lagomorph SAMD9 orthologs uniquely harbor a charge-reversal acidic residue at one of three sites, a change known to inactivate hSAMD9/9L. Here, we show that despite this variation, rabbit SAMD9 (rSAMD9) potently restricts vaccinia virus replication and specifically reduces tRNAPhe levels, mirroring hSAMD9. However, unlike hSAMD9, rSAMD9s minimal tRNase module extends beyond the homologous tRNase domain (amino acid 158-389) to include the SIR2 region. Additional basic residues, one unique to rSAMD9, were also found to be important for its antiviral activity. The crystal structure of rSAMD9158-389 closely resembles hSAMD9156-385, though with difference in loop conformations. These findings demonstrate that lagomorph SAMD9 preserves core tRNA-targeting and antiviral functions despite a key residue variation and the need for an extended tRNase module. AUTHOR SUMMARYSterile Alpha Motif Domain-containing 9 (SAMD9) and its paralog SAMD9-like (SAMD9L) are antiviral factors and tumor suppressors. Gain of function (GoF) mutations of SAMD9/9L, however, cause a spectrum of human diseases with immunological or/and neurological presentations. We recently identified the effector domain of SAMD9/9L as a previously unrecognized tRNase, a function critical for both their normal physiological roles and the pathogenic effects of by patient-derived mutations. We also identified three basic residues within the tRNase domain that are highly conserved across mammalian SAMD9/9L as key to its enzymatic and biological activities. However, lagomorph SAMD9 orthologs uniquely harbor a negatively charged acidic residue at one of three sites. Through extensive structural and functional analyses, here we demonstrate that rabbit SAMD9 (rSAMD9) retains both tRNA- cleaving and antiviral activities, despite notable differences in its tRNase module- including a unique basic residue specific to rSAMD9 and a larger domain architecture extending beyond the conserved tRNase core. These data highlight both the evolutionary conservation of tRNase activity in mammalian SAMD9/9L and the flexibility of the tRNase module within the protein family.

biochemistry↗

bioRxiv2025

Aging-dependent dysregulation of EXOSC2 is maintained in cancer as a dependency

Reprogramming of aged donor tissue cells into induced pluripotent stem cells (A-iPSC) preserved the epigenetic memory of aged-donor tissue, defined as genomic instability and poor tissue differentiation in our previous study. The unbalanced expression of RNA exosome subunits affects the RNA degradation complex function and is associated with geriatric diseases including premature aging and cancer progression. We hypothesized that the age-dependent progressive subtle dysregulation of EXOSC2 (exosome component 2) causes the aging traits (abnormal cell cycle and poor tissue differentiation). We used embryonic stem cells as a tool to study EXOSC2 function as the aging trait epigenetic memory determined in A-iPSC because these aging traits could not be studied in senesced aged cells or immortalized cancer cells. We found that the regulatory subunit of PP2A phosphatase, PPP2R5E, is a key target of EXOSC2 and this regulation is preserved in stem cells and cancer.

cell biology↗

bioRxiv2025

β-Arrestin Condensates Regulate G Protein-Coupled Receptor Function

G protein-coupled receptors (GPCRs) are the largest class of receptors in the genome and control many signaling cascades essential for survival. GPCR signaling is regulated by {beta}-arrestins, multifunctional adapter proteins that direct receptor desensitization, internalization, and signaling. While at many GPCRs, {beta}-arrestins interact with a wide array of signaling effectors, it is unclear how {beta}-arrestins promote such varied functions. Here we show that {beta}-arrestins undergo liquid-liquid phase separation (LLPS) to form condensates that regulate GPCR function. We demonstrate that {beta}-arrestin oligomerization occurs in proximity to the GPCR and regulates GPCR functions such as internalization and signaling. This model is supported by a cryoEM structure of the adhesion receptor ADGRE1 in a 2:2 complex with {beta}-arrestin 1, with a {beta}-arrestin orientation that can promote oligomerization. Our work provides a paradigm for {beta}-arrestin condensates as regulators of GPCR function, with LLPS serving as an important promoter of signaling compartmentalization at GPCRs.

cell biology↗

bioRxiv2025

JACUZI-SD: An automated, high-throughput, minimally stressful approach to sleep depriving larval zebrafish.

While sleep deprivation broadly disrupts health and well-being, the neural and molecular mechanisms that signal increased sleep pressure remain poorly understood. A key obstacle to progress is the fact that traditional methods for inducing sleep deprivation (SD) in animal models often introduce confounding stress or disrupt circadian rhythms. Here, we present JACUZI-SD (Jetting Automated Currents Under Zebrafish to Induce Sleep Deprivation), a fully automated, high-throughput system designed to induce sleep deprivation in larval zebrafish with minimal stress. By delivering randomized water pulses via a custom milli-fluidic device integrated with a 96-well plate and controlled by an Arduino, JACUZI-SD promotes wakefulness during the natural dark cycle without the stress associated with existing SD methods. Our results demonstrate that JACUZI-SD reduces total sleep time by 41-64% and elicits a robust rebound sleep characterized by increased sleep bout length following deprivation. Importantly, this method avoids activating the hypothalamic-pituitary-interrenal (HPI) stress axis, as evidenced by reduced stress marker expression compared to other deprivation methods. Additionally, the system reliably activates established sleep pressure pathways, including the upregulation of galanin in the neurosecretory preoptic area, while also revealing biologically relevant inter-individual variability in homeostatic rebound responses. JACUZI-SD provides a powerful, minimally invasive platform for dissecting the neural and molecular underpinnings of sleep homeostasis in vertebrates.

neuroscience↗

bioRxiv2025

QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organism Genomes

Despite the increasing number of genomes, the annotation of protein-coding genes is still lacking. In some genomes where transcriptome data is not available, various tools have been developed to annotate genes based on homologous proteins, but each tool has its limitations. Here, we propose quickprot, a user-friendly command-line tool that constructs a set of redundancy-free gene models from the target genome based on the homologous protein sequences of a set of closely related species. We tested its applicability in stonefish, and the results showed that it has high accuracy and runs faster than existing tools. This low-cost, high-precision annotation method is expected to become a useful tool for genome annotation, which will contribute to the research of comparative genomics. The software is implemented in Python and licensed under the MIT License. The source code, documentation, and tutorials can be obtained at https://github.com/thecgs/quickprot.

bioinformatics↗

bioRxiv2025

A reference genome assembly of the alpine forage grass Elymus nutans

Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species used for high yield artificial grassland planting because of its rich nutritional value and good palatability for herbivorous ruminant animals. In this study, using advanced sequencing technology, we generated an allohexaploid reference genome for E. nutans, representing the three sets of chromosomes (subgenomes St, Y, and H). This is the first study to our knowledge to confirm the origin of the Y subgenome, which shares a close relationship with the V subgenome. We predict that E. nutans arose via two-step hybridization and that its speciation occurred [~]3.16 MYA. The whole genome in this study will update the Triticeae family genomics information and provide theoretical basis for the evolutionary of its related speicies.

plant biology↗

bioRxiv2025

Molecular Mechanisms of Chinese Medicine in Regulating Colorectal Cancer Immune Microenvironment: Insights from Single-Cell Transcriptomics and Network Pharmacology

BackgroundThe molecular mechanisms underlying the efficacy of Traditional Chinese Medicine (TCM) in colorectal cancer treatment remain largely unexplored. We developed a computational systems biology approach integrating single-cell transcriptomics with network pharmacology to elucidate the potential mechanisms of TCM in modulating colorectal cancer progression. MethodsWe developed an integrated computational pipeline for multi-omics data analysis combining single-cell transcriptomics with network pharmacology. Raw single-cell RNA-seq data from 3 normal tissues and 3 colorectal tumors were obtained from GEO database and processed using a customized workflow in R. Quality control, normalization, and dimensionality reduction were performed using the Seurat v4.0 algorithm, followed by unsupervised clustering to identify cell subpopulations. Differentially expressed genes (DEGs) were identified using MAST algorithm with adjusted p-value < 0.05 and |log2FC| > 1.0. These computationally identified DEGs were subsequently mapped to a comprehensive Traditional Chinese Medicine (TCM) database using a network pharmacology approach to predict herb-target interactions. In parallel, we integrated TCGA RNA-seq data (STAR-counts) with clinical information, applying log2(TPM+1) transformation for normalization. We then implemented a machine learning-based correlation analysis to construct gene-cell-immunity-pathway networks, using weighted gene co-expression network analysis (WGCNA) to identify key regulatory modules. ResultsOur computational analysis of single-cell RNA-seq data identified 109 differentially expressed genes (DEGs) that define the molecular signature of colorectal cancer microenvironment. Clustering algorithms revealed 14 distinct cell subpopulations, with predominant immune cell infiltration, particularly B and T lymphocytes, suggesting a complex immune regulatory network. Network pharmacology analysis mapped these DEGs to potential therapeutic targets, computationally predicting interactions with 140 traditional Chinese herbs. These herbs were classified into 8 functional categories. Through integrative multi-omics analysis and pathway enrichment algorithms, we identified core regulatory networks comprising 23 genes and 39 significantly enriched signaling pathways (FDR < 0.01) that orchestrate immune cell function in the tumor microenvironment. Notably, our analysis in silico revealed previously uncharacterized gene-pathway interactions that may explain the immunomodulatory effects of specific herbal compounds. ConclusionsOur systems biology and computational analysis revealed a potential mechanism by which 8 categories of Chinese herbal medicines and 23 genes across 39 signaling pathways may regulate colorectal cancer progression through modulation of specific gene regulatory networks and immune cell functions. These findings demonstrate the value of integrative computational approaches in elucidating complex biological mechanisms of traditional medicines

immunology↗

bioRxiv2025

A study of different pre-treatment methods for cigarettes and their aroma differences

The study innovatively utilized a combination of smoking machine and Cambridge filter to effectively extract the aroma compounds generated during smoking of cigarettes, and employed three different pretreatment methods to obtain optimal cigarette pretreatment procedures. In addition, the aroma components of different cigarettes were identified by different instruments such as gas chromatography-mass spectrometry. Combined with the calculation of Odor Activity Values (OAV), PCA analysis and sensory evaluation were performed on the five types of cigarettes to reveal differences and similarities in their aroma profiles.

biochemistry↗

bioRxiv2025

deepTFBS: Improving within- and cross-species prediction of transcription factor binding using deep multi-task and transfer learning

The precise prediction of transcription factor binding sites (TFBSs) is crucial in understanding gene regulation. In this study, we present deepTFBS, a comprehensive deep learning (DL) framework that builds a robust DNA language model of TF binding grammar for accurately predicting TFBSs within and across plant species. Taking advantages of multi-task DL and transfer learning, deepTFBS is capable of leveraging the knowledge learned from large-scale TF binding profiles to enhance the prediction of TFBSs under small-sample training and cross-species prediction tasks. When tested using available information on 359 Arabidopsis TFs, deepTFBS outperformed previously described prediction strategies, including position weight matrix, deepSEA and DanQ, with a 244.49%, 49.15%, and 23.32% improvement of the area under the precision-recall curve (PRAUC), respectively. Further cross-species prediction of TFBS in wheat showed that deepTFBS yielded a significant PRAUC improvement of 30.6% over these three baseline models. deepTFBS can also utilize information from gene conservation and binding motifs, enabling efficient TFBS prediction in species where experimental data availability is limited. A case study, focusing on the WUSCHEL (WUS) transcription factor, illustrated the potential use of deepTFBS in cross-species applications, in our example between Arabidopsis and wheat. deepTFBS is publically available at https://github.com/cma2015/deepTFBS. One sentence summaryThe high-performing deep learning framework deepTFBS can flexibly perform within- and cross-species prediction of TF binding, transferring the transcription regulation from model to non-model species.

bioinformatics↗

bioRxiv2025

High-resolution NMR spectroscopy of proteins in intact mitochondria

Understanding protein structure and function within mitochondria is essential for unraveling the molecular mechanisms underlying cellular energy production, stress response, and disease. Here, we present a novel approach for NMR observation of proteins within intact mitochondria by delivering proteins directly into isolated mitochondria via electroporation. Using this method, we investigate the interaction of -synuclein (-syn) with the mitochondria membrane and examine how post-translational modifications regulate this interaction. Additionally, we assessed the stability of GB1 and the dimerization of its variant within mitochondria, achieving quantitative insights into mitochondrial environmental impact on protein function. This approach offers a valuable framework for exploring mitochondrial related biomolecular events at atomic-resolution within intact mitochondria, paving the way for a more comprehensive understanding of the molecular events governing mitochondrial health and dysfunction.

biochemistry↗

bioRxiv2025

Discovery, characterization, and application of chromosomal integration sites in the hyperthermophilic crenarchaeon Sulfolobus islandicus

Sulfolobus islandicus, an emerging crenarchaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has considerably limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs (crRNAs) targeting eight chromosomal integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. By leveraging the endogenous CRISPR-Cas systems, we integrated the reporter gene lacS into these sites and validated heterologous gene expression through a {beta}-galactosidase reporter assay, which revealed significant positional effects on expression levels. As a proof of concept, we utilized these characterized sites to genetically manipulate lipid ether composition by overexpressing GDGT (glycerol dibiphytanyl glycerol tetraether) ring synthase B (GrsB) in S. islandicus, a key enzyme in GDGT biosynthesis. This study expands the genetic toolbox for S. islandicus and highlights a concept that could be widely applicable to other Sulfolobales, advancing their potential as robust platforms for archaeal synthetic biology and industrial biotechnology.

synthetic biology↗

bioRxiv2025

Stathmin 1 regulates mitophagy and cellular function in hematopoietic stem cells

Stathmin 1 is a cytoplasmic phosphoprotein that regulates microtubule dynamics via promotion of microtubule catastrophe and sequestration of free tubulin heterodimers. Stathmin 1 is highly expressed in hematopoietic stem cells (HSCs), and overexpressed in leukemic cells, however its role in HSCs is not known. Herein, we found that loss of Stathmin 1 is associated with altered microtubule architecture in HSCs, and markedly impaired HSC function. Transcriptomic studies suggested alterations in oxidative phosphorylation in Stmn1-/- HSCs, and further mechanistic studies revealed defective mitochondrial structure and function in the absence of Stathmin 1 with increased ROS production. Microtubules associate with mitochondria and lysosomes to facilitate autophagosome formation and mitophagy, and indeed we found that this critical mitochondrial quality control process is impaired in Stathmin 1-deficient HSCs. Finally, stimulation of autophagy improved the colony forming ability of Stmn1-/- hematopoietic stem and progenitor cells. Together, our data identify Stathmin 1 as a novel regulator of mitophagy and mitochondrial health in HSCs. Key PointsO_LIThe microtubule regulating protein Stathmin 1 is highly expressed in HSPCs and promotes normal microtubule architecture. C_LIO_LILoss of Stathmin 1 in HSPCs leads to impaired autophagy with abnormal mitochondrial morphology, decreased respiratory capacity, and impaired cellular function. C_LI

cell biology↗

bioRxiv2025

SlicerMorph Photogrammetry: An Open-Source Photogrammetry Workflow for Reconstructing 3D Models

1. ContextAccurate three-dimensional (3D) models of skeletal and other biological specimens are crucial for ecological and evolutionary research and teaching. Here, we present a streamlined, open-source workflow for 3D photogrammetry that allows researchers to construct 3D models using the 3D Slicer and the SlicerMorph ecosystem. 2. Objectives and MethodsWe present an updated photogrammetry pipeline within the 3D Slicer ecosystem that combines advanced image masking via Segment Anything Model (SAM) with the open-source ODM reconstruction engine. Our approach systematically reduces artifacts in delicate cranial regions by automating background removal. We validate this pipeline against micro-CT references using multiple rodent skull specimens, quantifying accuracy through mean distance, root mean square error (RMSE), Hausdorff distance, and Chamfer distance. 3. ResultsOur method consistently reduces average surface error by 10-15% compared to a previous open-source photogrammetry workflow. This gain is particularly pronounced around thin or fenestrated anatomical structures such as zygomatic arches, where the previous workflow created the most noise. Although occasional increases in Hausdorff distance reflect localized photography gaps, improved mean distance and RMSE underscore improved overall fidelity. 4. Main ConclusionsThe 3D Slicer Photogrammetry extension provides a robust, fully open-source solution for generating high-quality 3D reconstructions from photographs. The streamlined pipeline lowers technical barriers to collecting reliable 3D data and fosters reproducible research across diverse biological collections.

evolutionary biology↗

bioRxiv2025

ARIH1 deficiency impairs spatial learning and memory via GIRK2 upregulation in hippocampal CaMKII-expressing neurons in mice

Alterations of Ariadne RBR E3 Ubiquitin Protein Ligase 1 (ARIH1), a human homologue of Drosophila Ari, have been associated with a number of human diseases. Given the importance of ubiquitin-proteasome system in learning and memory, whether ARIH1 involves in the process has not been explored. Here we report that ARIH1-deficent mice exhibited a defect in learning and memory evidenced in Morris water maze and in novel object recognition tests without changes in basal motor activity, anxiety, and depressive behaviors. We found that ARIH1 deficiency resulted in an upregulation of G protein-gated inwardly rectifying potassium channel 2 (GIRK2) in dorsal hippocampus that was attributed to the impaired ubiquitination and degradation. Locally injection of ARIH1-expressing lentivirus to restore the ARIH1 expression of dorsal hippocampus in ARIH1+/- mice restored the impaired learning and memory. Moreover, selective knockdown ARIH1 in dorsal hippocampal calcium-calmodulin-dependent protein kinase II (CaMKII)-expressing neurons, but not for parvalbumin+ (PV) or somatostatin+ (SST) neurons, in naive mice was sufficient to mimic the damage in learning and memory of ARIH1+/- mice. Lastly, we demonstrated that systemically or locally inhibition of GIRK activity was able to improve ARIH1 deficiency-induced decline of learning and memory in ARIH1+/- mice. The present study discovered the clear role of ARIH1 in mediating learning and memory, defect of ARIH1 resulted in upregulation of GIRK2 in hippocampal CaMKII-expressing neurons via modulating the ubiquitination and degradation GIRK2.

neuroscience↗

bioRxiv2025

Coenzyme Q10 alleviates the mitochondrial damage by high-fat load in hepatocytes of spotted seabass (Lateolabrax maculatus) via promoting mitophagy

Coenzyme Q10, as a natural fat-soluble compound, can play a role in protecting mitochondria, but the mechanism is still unclear. Here, we explored the mechanism of coenzyme Q10 enhancing mitochondrial function using hepatocytes of spotted seabass. Three groups were set: normal medium as control group, fatty acid group containing 100 mol/L FA (FA group), and 100 mol/L FA and 5 mol/L coenzyme Q10 group (FA+COQ10). After the culture, the results showed that FA treatment significantly increased the triglyceride content in the cells. Bodipy staining showed that many lipid droplets appeared in the FA group, while coenzyme Q10 reduced triglycerides content and lipid droplets. Moreover, coenzyme Q10 significantly reduced the content of ROS in cells. After scavenging ROS, the liver cell damage caused by FA was alleviated, the mitochondrial membrane potential and its mitochondrial metabolic enzyme activity were restored, and the ATP content was increased. Further analysis showed that FA significantly down-regulated the expression of mitophagy key genes pink, parkin and lc3b, while up-regulated the expression of p62. Through mitochondrial fluorescence staining and mtDNA content detection, it was found that the number of mitochondria in FA-treated cells decreased significantly, while the number of mitochondria increased significantly after FA+COQ10 treatment. This indicates that coenzyme Q10 can significantly promote the mitophagy process. In order to further study whether the enhancement of mitochondrial function by coenzyme Q10 is related to the activation of autophagy, we set up FA group, FA+COQ10 group and FA+COQ10+Mdivi-1 group (pretreatment with mitophagy inhibitor Mdivi-1). After Mtphagy Dye staining, it was found that the number of autophagosomes in the FA+COQ10+Mdivi-1 group was lower than that in the FA+COQ10 group, indicating that the activation of mitophagy by coenzyme Q10 was inhibited. The results of this study indicate that coenzyme Q10 enhances mitochondrial function and alleviates excessive fat deposition dependent on PINK1-mediated mitophagy.

cell biology↗