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Shi, M.

Publications and source records attributed to Shi, M..

At least 19 recordsLinked to original sources

Imaging biological tissue at extended depth using swept-source visible-light OCT

We present a swept-source visible-light optical coherence tomography (SS-vis-OCT) system with twice the imaging depth of prior SS-vis-OCT and improved sensitivity for imaging biological samples, achieving shot-noise-limited operation. Because second-harmonic generation is limited by the booster optical amplifier's output power, the visible-light SS power is capped at 450 W. Increasing it further would require a more powerful, but costlier, amplifier. Instead, we reduce the receiver noise floor by selecting a balanced detector with NEP approaching the thermal (Johnson-Nyquist) limit. Real-time numerical k-linearization increases the effective number of linear-in-wavenumber samples per sweep, further improving SNR and extending the imaging range. Together, these improvements yield a sensitivity of 89 dB and an imaging depth of 9 mm in air or 6.5 mm in tissue, enabling full anterior-segment imaging of ex vivo porcine eyes.

bioengineering↗

Flexible 3D multimodal organoid interface reveals functional subnetworks and coordinated circuit activity in cortical organoids

The balance between excitatory and inhibitory (E/I) neurons is fundamental to cortical function, and its disruption underlies a wide range of neurological disorders, including epilepsy, Alzheimers disease and autism spectrum disorder. Cortical organoids offer a promising model to study this balance, as they recapitulate key features of brain development, including the emergence of E/I circuitry. However, no existing technology can simultaneously resolve neuronal identity, spatial organization, and dynamic network activity within intact organoids, limiting precise interrogation of E/I circuit function. Here, we report INFORM, an INtegrated Flexible Organoid Recording Multimodal neural interface that conformally wraps organoids of any size and shape, enabling long-term recordings over 371 days with above 90% of channels detecting spikes. INFORM interface combines four distinct modalities; electrophysiology, two-photon calcium imaging, targeted electrical microstimulation, and chemical intervention to monitor and modulate neural activity across multiple spatial and temporal scales spanning from action potentials from single neurons to synchronized bursts from large-scale populations. Such high-resolution interrogation enables probing of emergence of functional connectivity in fusing assembloids and resolves spatially discrete functional subnetworks that can be selectively recruited and modulated by INFORM. Neurotransmission blockade confirms that stimulus-evoked suppression of neuronal spiking is mediated by GABAergic inputs providing direct functional evidence of the presence of inhibitory signaling in organoids. This work allows single-cell dissection of functional networks in brain organoids, providing a powerful platform for modelling and studying cortical development, neurological diseases, and the E/I imbalances underlying circuit dysfunction.

neuroscience↗

Metatranscriptomic surveillance reveals overlooked liver-associated parasite diversity and broad host ranges in small mammals from southern China

Parasite communities in the internal organs of small mammals remain poorly characterized because metatranscriptomic pathogen discovery has largely focused on viruses and bacteria. We individually sequenced liver transcriptomes from 351 small mammals collected across 14 cities in Guangdong Province, China, and combined sequence-based detection with phylogenetic, abundance, transcriptional, and morphological analyses. Parasites were detected in 148 animals (42.2%). Four liver-associated taxa were identified, including three putatively novel or highly divergent lineages. Trichinellidae sp1 dominated the community, occurring in 36.2% of animals (127/351), five host species spanning Rodentia and Eulipotyphla, and all surveyed cities. Hydatigera taeniaeformis occurred in 3.7% (13/351), and its identification was supported by hepatic cysts and morphologically recovered strobilocerci. Eucoccidiorida sp1 and Trypanosoma sp1 were detected sporadically. Mapping to available reference genomes revealed transcripts from multiple genes and functional categories, supporting genuine biological signals rather than isolated marker-gene matches. Amsterdam virus covaried with Trichinellidae sp1 (r = 0.59), whereas Wenzhou tapeworm virus 1 covaried with H. taeniaeformis (r = 0.47). These findings reveal an unexpectedly prevalent, phylogenetically diverse, and broadly distributed liver-associated parasite community and establish individual-organ metatranscriptomics as a useful framework for parasite discovery and surveillance.

microbiology↗

Multi-kingdom microbial diversity and interaction landscapes in mosquitoes revealed by 5,163 individual meta-transcriptomes

Mosquitoes are pathogen vectors embedded within diverse microbial ecosystems. However, the nature and interactions among their multi-kingdom microbiome remain poorly understood. We conducted a nationwide single-mosquito meta-transcriptomic survey of 5,163 mosquitoes representing 100 species across China, integrating viral discovery with marker-gene profiling of bacteria, archaea, fungi, and other eukaryotic microbes. From this, we identified 1,606 microbial species-level taxa, including extensive novel diversity, and revealed pronounced host species-specific organization of mosquito-associated communities. We detected 34 pathogens or potential pathogens of human or animal relevance, whose prevalence, abundance, host range, and geographic distribution defined distinct epidemiological patterns. Network analysis uncovered pervasive cross-kingdom microbial associations, including candidate antiviral relationships involving Wolbachia and other microbial taxa. Our study establishes a detailed view of the full-spectrum microbiome and provides a resource and conceptual framework for studying vector competence, pathogen emergence, and microbiome-informed mosquito-borne disease control.

microbiology↗

An orally administered peptide hydrogel disentangles immune-microbiota crosstalk for long-term ulcerative colitis therapy

Ulcerative colitis (UC) is a global health challenge driven by immune dysregulation and gut microbiota imbalance.1 Current treatments, limited by insufficient efficacy and systemic toxicity during prolonged use, fail to resolve the intertwined immune-microbial pathology.2 Here, we report an orally administered self-assembled hydrogel C2-(IIRR)2I-NH2 (CIR), engineered from host defense peptides, which disrupts the immune-microbiota entanglement. The CIR hydrogel exhibits structural transformation at the inflamed sites rich in liposaccharide (LPS), a pro-inflammatory molecule derived from pathogenic bacteria. Stable {beta}-sheet nanofibers can transfer to bioactive -helix conformations, enabling localized therapeutic action with minimal off-target toxicity. In murine colitis models, CIR restores mucosal integrity and suppresses disease severity, outperforming the first-line drug 5-aminosalicylic acid (5-ASA). Microbiome profiling reveals its capacity to rebalance gut microbiota, depleting LPS produced pathogenic bacteria like Prevotellaceae. Transcriptomic analyses further indicate that CIR silences TLR4-mediated signaling pathway. By synergistically targeting immune dysregulation and microbial dysbiosis, this self-assembled peptide hydrogel establishes a paradigm-shifting strategy for UC, offering clinically translatable potential for multifactorial gastrointestinal disorders.

bioengineering↗

From distyly to stigma-height dimorphism: phylogenetic insights into the evolutionary breakdown of distyly in Jasminum

Background and AimsDistylous polymorphisms (distyly) are adaptations for plants to improve efficiency of cross-pollination and reduce pollen wastage. Theoretical models suggest that distyly evolves from stylar monomorphism via an intermediate stage of stigma-height dimorphism (SHD), however, this evolutionary scenario is only observed in few distylous lineages. The genus Jasminum have many species exhibit either distyly or SHD, providing an ideal opportunity to test models of the evolution of distyly. Focusing on the evolution of distyly, we investigated floral morphs and evaluated the occurrence of distyly and SHD in Jasminum using phylogenetic reconstruction and morphological analysis. MethodsWe investigated floral morphs and evaluated the occurrence of distyly and stigma-height dimorphism through morphology observation. To perform phylogenetic analysis, we sequenced plastomes of forty species from Jasminum and Chrysojasminum using Illumina next generation sequencing, and then constructed phylogenetic tree using maximum likelihood method and Bayesian inference. Based on the phylogenetic tree, we inferred the ancestral floral type through ancestral reconstruction. Key ResultsOur results suggest that the distyly originated in the common ancestor of Jasminum and Chrysojasminum. SHD occurs in several Jasminum species scattered in different clades of the phylogenetic tree, suggesting multiple independent reversions from distyly back to SHD. However, this transition is not associated with the loss of ancillary polymorphisms, as all the species examined in this study well retain dimorphic traits for other floral organs such as pollens and stigmas. Moreover, most species maintain strict heteromorphic self-incompatibility, while J. officinale has lost or at least partially lost self-incompatibility, suggesting that distyly is not always linked to self-incompatibility. ConclusionsIn Jasminum, breakdown of distyly resulted in evolutionary transitions to stigma-height dimorphism for multiple times, suggesting that distyly is not a stable floral polymorphism under certain selective forces. These findings advance our understanding on the evolution of distyly and plant reproductive systems.

plant biology↗

Balancing performance and complexity of dual-wedge prism-based spectroscopic single-molecule localization microscopy

Spectroscopic single-molecule localization microscopy (sSMLM) enables multiplexed super-resolution imaging by simultaneously acquiring the spatial position and spectral information of individual fluorophores. Dual-wedge prism (DWP)-based implementations provide a compact, alignment-stable approach to spectral dispersion, but trade-offs between localization precision, spectral precision, and experimental complexity remain. We systematically compare five DWP-based sSMLM configurations, including two-dimensional (2D) and three-dimensional (3D) implementations using single DWP (DWP-sSMLM) and symmetrically-dispersed DWP (SDDWP-sSMLM). We evaluate lateral precision, spectral precision, and ease of use. SDDWP configurations acquire spectral images in both channels and utilize both for spatial localization, yielding the highest lateral and spectral precision. However, for applications that do not require axial information, 2D-DWP provides a simple, plug-and-play solution with robust performance. This work offers a guideline for selecting DWP configurations based on experimental needs.

bioengineering↗

Preclinical Characterization of Hippo pathway inhibition: Insights from Pharmacological and Genetic Studies

The Hippo pathway is an evolutionarily conserved regulator of growth, regeneration, and organ homeostasis, and while its dysregulation is well established in cancer, the effects of inhibiting this pathway on normal tissues are less understood. Here we have systematically investigated the impact of Hippo pathway inhibition by comparing pharmacologic perturbation using a covalent small-molecule TEAD inhibitor (TEADi CMPD1, also known as GNE-8025) with genetic suppression of YAP/TAZ. We identified three key target organs that consistently emerged upon TEAD inhibition: the kidney, as well as the pancreas, and thymus. Across models, both perturbations led to comparable disease phenotypes in these organs, including tubular degeneration in the kidney, acinar atrophy in the pancreas, and lymphoid depletion in the thymus. However, the extent of damage was more pronounced in mice treated with the small-molecule inhibitor, highlighting potential dose and compound specific effects while remaining broadly consistent with the phenotypes observed upon genetic ablation of YAP/TAZ. This highlights the key role of evaluating both genetic and pharmacological perturbations to characterize the phenotypes and potential toxicities when modulating novel targets in oncology. To further investigate the mechanisms underlying pan-TEAD inhibition and kidney related adverse effects, we further characterized this class effect through a comprehensive transcriptomic analysis of the kidney to map the pathways involved in renal response. SignificanceUnderstanding on target toxicities is critical for the safe clinical development of TEAD inhibitors. Here, by integrating pharmacologic TEAD inhibition with genetic suppression by developing a mouse model that characterizes systemic, inducible knockdown of YAP/TAZ, we provide a systematic framework to define the Hippo pathway liabilities in vivo. We identify kidney, pancreas, and thymus as conserved target organs with concomitant phenotypes across both genetic and pharmacological methods, establishing these as pathway driven effects. Importantly, we uncover dose dependent and partially irreversible injury, particularly in kidney and pancreas, alongside mechanistic insight linking TEAD inhibition to aldosterone signaling disruption in kidney. These findings highlight the importance of strategies to identify monitorable, manageable adverse effect to guide clinical translation of TEAD targeting strategies.

cancer biology↗

Regulation of protein abundance in neurons by selective translation of 3'UTR isoforms

The precise regulation of protein synthesis is essential for cellular function and survival. In particular, in neurons, dysregulated mRNA translation is linked to impaired memory formation and is a hallmark of neurodegenerative diseases. Neurons are characterized by tissue-specific, long 3' untranslated regions (3'UTRs); in this study, we demonstrate that mRNA isoforms with these neuronal 3'UTRs are less efficiently translated than their short counterparts in Drosophila and mammalian brains. 3'UTR-dependent translation is based on a negative feedback mechanism centered around the two neural-enriched proteins ELAV and Pumilio. The long elav 3'UTR inhibits production of the neuronal ELAV protein, which in turn mediates 3'UTR extension of hundreds of neuronal genes. Those long 3'UTR isoforms are preferentially bound and translationally inhibited by Pumilio. The regulatory loop maintains optimal neuronal 3'UTR and protein levels in conditions of genetic and environmental perturbations; its disruption reduces animal viability and lowers stress resilience, and causes severe developmental phenotypes in flies and in human brain organoids. We propose 3'UTR-mediated translational control as an evolutionarily conserved mechanism for the maintenance of cell-type-specific proteostasis.

molecular biology↗

Procedure-Matched Comparison of TNBS/Ethanol Enema and DSS Free-Drinking Models of Ulcerative Colitis in Rats: Immune Endotype Profiling and a Translational Model-Selection Framework

ObjectiveChoosing between TNBS/ethanol enema and DSS free-drinking water protocols for establishing rat ulcerative colitis(UC) models remains a practical challenge in preclinical research. Beyond confirming that both methods induce colitis, no prior study has quantified the independent contribution of enema procedural trauma to inflammatory readouts, reported sex-stratified cytokine responses, or formally linked model-specific immune profiles to human UC endotypes. MethodsTen SPF-grade SD rats(half male and half female) were allocated to a normal control, a procedure-matched saline enema control(anesthesia and enema without chemical agent), a TNBS group(100 mg/kg TNBS + 50% ethanol enema), and a DSS group(3% DSS free-drinking, 7 days). Endpoint assessments included body weight, colon length, macroscopic and histological scoring(modified Macpherson criteria, 0-10), and serum TNF- and IL-6 by ELISA. Post-hoc exploratory analyses included sex-stratified cytokine sub-analysis and coefficient of variation(CV%) for each readout. ResultsBoth model groups successfully induced UC(P<0.05 vs. controls for all endpoints). Critically, the procedure-matched saline enema control confirmed that colonic inflammation in the TNBS group was attributable to the chemical agent rather than mechanical trauma. TNBS induced significantly higher TNF-(90.2{+/-}10.5 vs. 73.5{+/-}9.8 pg/mL, P<0.05) and IL-6(66.5{+/-}8.3 vs. 53.2{+/-}7.6 pg/mL, P<0.05) than DSS,consistent with Th1-polarized vs. innate barrier-disruption immune endotypes, respectively. Coefficient of variation analysis indicated greater intra-group variability in TNBS versus DSS, reflecting the procedural dependency of enema-based models. ConclusionA procedure-matched control design is essential for valid TNBS-vs.-DSS comparisons and has been systematically underutilized in prior studies. Based on immune endotype alignment, TNBS is recommended for screening T-cell-targeted therapies and acute anti-inflammatory agents, while DSS is recommended for epithelial barrier repair and microbiome-modulating interventions. A model-selection decision framework derived from these data is provided to guide preclinical study design.

animal behavior and cognition↗

Alignment-free phylogenetic inference via hyperbolic protein language models

Conventional phylogenetic methods rely on multiple sequence alignments which are computationally intensive and often fail for highly divergent lineages. Here, we introduce LucaPhylo, an alignment-free framework that infers evolutionary relationships directly from unaligned sequences. Through a cascaded learning strategy LucaPhylo integrates protein language models with hyperbolic geometry, a representation space naturally suited to hierarchical branching, to capture deep evolutionary constraints without explicit homology matching. Using highly divergent RNA virosphere as a test case, LucaPhylo places unaligned sequences into phylogenetic trees with an accuracy comparable to leading alignment-based tree construction tools, while retaining divergent sequences that conventional pipelines frequently discard. It further enables the integration of divergent viral lineages into phylogenetic trees, thereby expanding the evolutionary landscape of RNA viruses. Together, LucaPhylo establishes an AI-driven, alignment-free paradigm for phylogenetic inference and provides a robust computational foundation for resolving deep evolutionary relationships among RNA viruses and other biological systems.

evolutionary biology↗

A sequence-based proactive intelligence for influenza antigenic profiling improves vaccine strain selection

Seasonal influenza viruses accumulate antigenic changes, eroding population immunity and necessitating recurrent vaccine updates. Hemagglutination inhibition (HI) assays are the standard for measuring antigenic relationships between circulating and vaccine strains; however, their limited throughput constrains the scale and timeliness of surveillance. Here, we present fluProfiler, a foundation-model-based framework that learns a stable mapping from viral sequences to antigenic space and uses this representation to support influenza antigenic prediction, vaccine strain evaluation, and diversity-driven sampling. fluAgPredictor aligns hemagglutinin (HA) and neuraminidase (NA) sequence representations with HI-derived antigenicity, enabling accurate and consistent inference of pairwise antigenic distances across surveillance-aligned evaluation settings. Without prior annotation of antigenic sites, it identifies key residues in immunodominant epitopes and reveals the cooperative contributions of HA and NA to antigenic variation. Building on this antigenic-space representation, fluVacSelector provides antigenic coverage scores that are concordant with World Health Organization (WHO) vaccine recommendations while also flagging potential candidates that may offer broader coverage ahead of formal consultations. fluAgEnhancer further leverages the same representation to prioritize antigenically informative and diverse strains for experimental characterization, achieving comparable predictive accuracy with approximately 25% fewer HI measurements than random sampling. Together, these modules provide a high-throughput and interpretable complement to HI testing, converting routine genomic surveillance into a more proactive, data-driven support system for antigenic monitoring and vaccine strain selection.

bioinformatics↗

A Haplotype-resolved Telomere-to-Telomere Pig Genome

Haplotype-resolved telomere-to-telomere (T2T) pig genomes have not been reported, but may be essential for xenotransplantation and interspecies chimerism. Here we describe fully phased paternal and maternal T2T assemblies of an Erhualian pig (Ssc_EHL), enabling chromosome-scale reconstruction at base resolution. We uncover 2,498 (paternal haplotype) and 2,577 (maternal haplotype) protein-coding loci previously unresolved in Sscrofa11.1, while maintaining high concordance for anchored gene models between haplotypes. Applying this haplotype-resolved T2T annotation to publicly available pig-to-human kidney xenograft transcriptomes further allows the resolution of xenograft cell states and reveals newly resolved, cell-type-enriched genes. Cross-species synteny and orthology analyses against human identified a subset of high-confidence pig-specific genes with limited human counterparts, thus, refining the genomic basis of interspecies divergence. By integrating these orthology features with organ transcriptomes, we further defined an Interspecies Chimerism Compatibility score to prioritize organ-enriched, highly conserved loci with minimal redundancy imbalance, providing haplotype consistent targets for engineering organ-deficient pigs. Together, this haplotype-resolved T2T pig genome provides a foundational resource for mechanistic studies and rational genome engineering in xenotransplantation and interspecies chimerism.

genomics↗

DNA-triggered AIM2 condensation orchestrates immune activation and regulation

The innate immune sensor AIM2 detects cytosolic DNA and initiates inflammatory responses, yet its activation mechanism remains incompletely understood. Here, we show that AIM2 undergoes liquid-liquid phase separation upon DNA binding, forming dynamic condensates both in vitro and in cells. These condensates serve as platforms for inflammasome and PANoptosome assembly, promoting immune activation across multiple pathways. Direct structural determination from condensates reveals the assembly of active-form ASC filaments. Mechanistically, liquid-phase condensation is governed by multivalent interactions involving different AIM2 domains, including previously uncharacterized regions and species-specific elements. In vitro and in vivo assays show that mutants specifically disrupting condensation impair immune complex assembly, cell death initiation, antimicrobial defense, and intestinal homeostasis. Moreover, AIM2-DNA condensates function as regulatory hubs targeted by host- and pathogen-derived factors to balance immune homeostasis or facilitate immune evasion. These findings establish liquid-phase condensation as a fundamental mechanism of AIM2 activation and a potential therapeutic target.

immunology↗

PRMT5-Mediated Arginine Methylation of HSP90AA1 Drives Esophageal Squamous Cell Carcinoma Progression

Dysregulated HSP90AA1 chaperone activity is a hallmark of multiple human cancers, yet its post-translational modifications in esophageal squamous cell carcinoma (ESCC) are poorly defined. Here, we identify a PRMT5-driven modification of HSP90AA1, symmetric dimethylation at arginine 182 (R182), as a pivotal switch that fuels ESCC progression. HSP90AA1 physically associates with PRMT5, and genetic or pharmacologic PRMT5 blockade diminishes HSP90AA1-R182 methylation and downstream oncogenic signaling. Functionally, HSP90AA1 loss suppresses ESCC cell proliferation, migration, and invasion; enforces cell cycle arrest and reverses epithelial-mesenchymal transition (EMT). Re-expression of wild-type HSP90AA1 rescues cancer cell growth and EMT in vitro and in vivo, whereas the methylation-deficient R182A mutant does not. Furthermore, clinically oriented analysis shows HSP90AA1 overexpression in ESCC tissues and indicates moderate prognostic utility. Moreover, dual targeting of the PRMT5/HSP90AA1 axis is therapeutically attractive, and combined PRMT5/HSP90AA1 inhibition acts synergistically to exert anti-tumor activity, markedly reducing clonogenicity, invasion, and tumor burden in both cell-derived and patient-derived xenograft models. These findings demonstrate that PRMT5/HSP90AA1 serve as mechanistic drivers and actionable biomarkers in ESCC and provide a rationale for biomarker-guided co-inhibition of PRMT5/HSP90AA1 in translational studies.

cancer biology↗

UBE3C retrofits the proteasome to enforce degradation of ultra-stable folds

Neurodegeneration and proteinopathies arise from mutated or misfolded proteins that form ultra-stable, proteotoxic aggregates that evade proteasomal degradation despite ubiquitylation1-8. These conditions are exacerbated by the deubiquitylase USP14 that can prematurely rescue substrates9-11. To counter these obstacles to effective proteolysis, eukaryotes evolved the highly conserved HECT-type E3 ligase UBE3C--dysregulated in neurodegeneration12,13 and overexpressed in cancers14-17--to reprogram the 26S proteasome toward heightened activity via unknown mechanisms18-25. Here we visualized functional dynamics of the human UBE3C-retrofitted proteasome enforcing degradation of a re-engineered superfolder GFP that normally escapes proteolysis, using time-resolved cryo-electron microscopy. A continuum of non-equilibrium conformations, comprising fourteen proteasome conformers orthogonally combined with four UBE3C states or three USP14 states, reveals a cryptic UBE3C-receptor site in the proteasomal lid and captures key intermediates of ubiquitin-chain elongation and branching at four linkage-specific ubiquitin-binding sites. Remarkably, UBE3C creates an extreme shortcut for ubiquitin shuttling that bypasses USP14, promotes USP14 recycling and allosterically strengthens substrate-unfolding forces of the AAA-ATPase unfoldase to ultimately surmount the unfolding energy barrier of ultra-stable proteins. These findings define the complete functional cycle of the UBE3C-reprogrammed proteasome, illuminating how UBE3C simultaneously controls USP14 and the proteasome to enforce clearance of ultra-stable folds, and establish crucial mechanistic foundations for proteolysis-targeting therapeutic discovery.

biochemistry↗

Systematic Analysis of Human Tissue- and Cell-Specific Metabolic Models Identifies High-Sugar, High Fat Diet Induced Liver Dysregulation

Human tissues exhibit specialized metabolic functions that are essential for maintaining whole-body metabolic homeostasis. To systematically characterize organ- and cell-type-specific metabolic heterogeneity, we constructed 32 tissue-specific and 81 cell-type-specific enzyme-constrained genome-scale metabolic models (ecGEMs) by integrating the global human metabolic network with the tissue- and single-cell transcriptomic data from the Human Protein Atlas (HPA). Our analysis revealed pronounced differences in metabolic network architecture and activity across the human body, identifying key cell types that drive tissue metabolic functions. To demonstrate the applicability of these models, we employed the liver-specific ecGEM to investigate the metabolic reprogramming induced by a high-sugar, high-fat (HSHF) diet, a primary driver of metabolic dysfunction-associated fatty liver disease (MAFLD). Flux balance analysis revealed a fundamental transition in hepatic metabolism: from a flexible, multi-functional system toward a constrained, lipid-centric regime. This state is characterized by carbohydrate and lipid overload, mitochondrial respiratory dysfunction, and a compromised capacity for reactive oxygen species (ROS) detoxification. These computational predictions were validated through integrative analysis of transcriptomic data from a human MAFLD cohort and metabolomic profiles from an in vivo HSHF rat model. Together, this work provides a comprehensive atlas of human metabolic models, enabling the systematic investigation of metabolic features across tissues and conditions from a systems-level perspective. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/706568v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1015c7org.highwire.dtl.DTLVardef@5c200org.highwire.dtl.DTLVardef@3c982org.highwire.dtl.DTLVardef@a2894d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Differential higher-order superassembly of HECT-type UBE3 ligases controlled by calcium signals

The yeast E4 ligase Hul5 transiently associates with the proteasome during heat shock and proteotoxic stress to maintain cytosolic protein quality control. Two of its human orthologs, UBE3B and UBE3C, have specialized to safeguard mitochondria and inherit Hul5 function, respectively. We determined cryo-electron microscopy structures of full-length human UBE3B and UBE3C in complex with calmodulin at 2.9-3.5 [A] in calcium-free and calcium-saturated conditions. Calmodulin acts as an inter-protomer molecular glue clamping UBE3B into ring-shaped anti-parallel homodimers or asymmetric trimers, and remodels UBE3C into a conformation competent for proteasome association. Calcium binding to calmodulin promotes disassembly of these higher-order complexes, toggling UBE3B/C from E4 to E3 activity. These findings reveal how calmodulin regulates higher-order architectures of E3/E4 ligases to rewire the ubiquitin-proteasome system via calcium signaling.

biochemistry↗