Biology subjects

Li, W.

Publications and source records attributed to Li, W..

At least 163 records · Page 9Linked to original sources

bioRxiv2026

Schizosaccharomyces orthogroup (SOG) resource: a web platform for exploring gene conservation in fission yeasts

The fission yeast Schizosaccharomyces pombe is a prominent model organism widely used to investigate fundamental cellular mechanisms. In addition to S. pombe, the genus Schizosaccharomyces includes six other species--S. octosporus, S. japonicus, S. cryophilus, S. osmophilus, S. lindneri, and S. versatilis. These fission yeast species share a common ancestor from which the genus diversified over more than 200 million years. This extensive evolutionary divergence provides opportunities for comparative genomics. Here, we present the Schizosaccharomyces orthogroup (SOG) resource, a web platform developed from our high-quality genome assemblies, gene annotations, and orthology assignments. Most fission yeast genes are assigned to one of over 5,000 orthogroups. The platform enables users to visualize orthogroup sequence alignments and phylogenetic trees, retrieve coding and flanking sequences, and explore the conservation of local synteny. This resource will benefit researchers focusing on individual genes as well as those investigating gene evolution at broader scales. It is freely accessible at https://www.sogweb.org. TAKE AWAYO_LIThe SOG resource covers all known species of Schizosaccharomyces. C_LIO_LIThe platform is built on high-quality genome assemblies and annotations. C_LIO_LIMost genes are assigned to one of over 5,000 orthogroups. C_LIO_LIUsers can view and explore alignments, phylogenetic trees, and local synteny. C_LIO_LIThis free resource aids functional and evolutionary research. C_LI

genomics↗

bioRxiv2026

Federated single-cell QTL meta-analysis reveals novel disease mechanisms

Genetic effects on gene expression are often cell type-specific and obscured in bulk analyses. To resolve this context-dependent regulation, we performed a federated cis-eQTL meta-analysis across 12 PBMC datasets (2,032 individuals, 2.5 million cells). Across six immune cell types, we identified cis-eQTLs for 6,592 genes and fine-mapped 14,985 independent loci. Notably, the 42% of eQTLs that were undetected in a bulk eQTL study on 43,301 whole blood samples also showed stronger enrichment for disease GWAS loci. We further identified three genome-wide significant and 65 suggestive loci affecting the abundance of (rare) immune cell types and validated these using previously reported hematological GWAS and bulk-derived trans-eQTLs. Integrating single-cell cis-eQTLs with bulk trans-eQTLs enabled us to anchor 6,382 trans-eGenes (37.2% novel) to upstream regulators and reconstruct directed gene regulatory relationships. For example, a hemorrhoidal disease-associated variant showed a CD4+ T cell-specific cis-eQTL on BACH1 that colocalized with 45 immune and metabolic trans-eGenes. These results demonstrate the power of single-cell QTL meta-analysis in interpreting complex trait genetics.

genetics↗

bioRxiv2026

Biosynthesis of 14-membered cyclopeptide alkaloids via non-heme-iron- and 2-oxoglutarate-dependent oxidative decarboxylation

Cyclopeptide alkaloids are an expanding class of plant peptide natural products defined by a macrocyclic ether-crosslink via a tyrosine-derived phenol. Classical cyclopeptide alkaloids are characterized by strained 13-to 15-membered cyclophanes and terminal modifications such as N-methylation and C-terminal styrylamine moieties. While synthetic access to many classical cyclopeptide alkaloids has been established, no biosynthetic route has been reported. Here, we elucidate the biosynthetic pathway of a 14-membered cyclopeptide alkaloid, lotusine A, from Chinese date tree (Ziziphus jujuba) which features peptide cyclization on a ribosomal precursor peptide by a split burpitide cyclase, non-heme-iron and 2-oxoglutarate-dependent oxidative decarboxylation affording the C-terminal hydroxystyrylamine, and SAM-dependent N-terminal -N,N-dimethylation. We apply discovered Z. jujuba enzymes in combination with a clubmoss cyclopeptide alkaloid cyclase for biosynthesis and diversification of analgesic adouetine X and anxiolytic sanjoinine A by combining in planta and in vitro reactions. Our work expands the biocatalytic repertoire of non-heme-iron- and 2-oxoglutarate-dependent enzymology to oxidative peptide decarboxylation and primes scaled metabolic engineering and chemoenzymatic synthesis of 14-membered cyclopeptide alkaloids with terminal posttranslational modifications.

biochemistry↗

bioRxiv2026

Converting Lysosomes into Photothermal Organelles Enables Nanoparticle-Free Tumor Ablation via Intracellular Vapor Bubbles

Photothermal nanomaterials enable precise tumor ablation but face limitations in biodistribution, tissue penetration, toxicity, and biodegradability. Here, we present a unique concept for nanoparticle-free photothermal therapy based on the lysosomal entrapment of cationic amphiphilic small molecular dyes for spatially controlled vapor bubble (VB)-mediated tumor cell ablation. This strategy, which exploits a universal biological and physical effect, employs intracellular pH gradients for extensive local dye enrichment in acidified organelles, transforming them into transient endogenous nanosized photothermal reactors for subsequent light activation. Using sunitinib, a clinically approved lysosomotropic anticancer drug, and the commercially available dye LysoTracker Deep Red, lacking intrinsic anticancer activity, we demonstrate pulsed laser-induced VB formation specifically from dye-loaded lysosomes, leading to selective photomechanical disruption of various cancer cell models across 2D cultures, 3D spheroids, patient-derived neuroblastoma tumoroids and tumor fragments from an ovarian carcinoma patient. This approach allows precise, low-fluence and wavelength-tunable cancer tissue ablation without the need for synthetic photoresponsive nanoparticles.

bioengineering↗

bioRxiv2026

Full-length transcriptome atlas of Panax vietnamensis var. fuscidiscus reveals novel genes and alternative splicing in tissue-specific biosynthesis of ocotillol-type saponins

BackgroundPanax vietnamensis var. fuscidiscus is the only known Panax species that accumulates exceptionally high levels of ocotillol (OCT)-type ginsenosides, particularly majonoside R2. However, the molecular mechanisms underlying OCT-type ginsenoside biosynthesis remain largely uncharacterized, due in part to the absence of comprehensive full-length transcriptome data and complete gene annotations. ResultsWe combined PacBio single-molecule real-time (SMRT) and Illumina RNA sequencing (RNA-Seq) technologies to construct the first tissue-specific, full-length transcriptome atlas of P. vietnamensis var. fuscidiscus. A total of 281,468 non-redundant transcripts were assembled, including 8,089 novel genes not present in existing annotations, substantially expanding the documented gene repertoire of this species. We identified 21 candidate genes putatively involved in triterpenoid saponin biosynthesis and uncovered distinct tissue-specific expression patterns across the oleanane (OA)-, protopanaxadiol (PPD)-, protopanaxatriol (PPT)-, and OCT-type biosynthetic pathways. Notably, we detected 46,917 alternative splicing (AS) events, with over 45% of expressed genes producing multiple isoforms. Several key biosynthetic genes--including dammarenediol synthase (DDS), cytochrome P450 716A53v2 (CYP716A53v2), and mevalonate diphosphate decarboxylase (MVD)--exhibited tissue-specific splicing patterns, such as retained introns and exon skipping, which may contribute to functional diversification of isoforms involved in OCT-type ginsenoside biosynthesis. These results highlight the importance of post-transcriptional regulation and transcript diversity in the evolution and fine-tuning of specialized metabolic pathways. ConclusionsThis study establishes a high-quality, full-length transcriptomic resource for P. vietnamensis var. fuscidiscus, revealing previously undescribed genes and extensive alternative splicing events related to ginsenoside biosynthesis. Our findings provide novel molecular insights into the mechanisms regulating OCT-type saponin accumulation and offer a foundation for future research into the functional characterization, regulatory mechanisms, and synthetic biological production of rare triterpenoid saponins.

plant biology↗

bioRxiv2026

Carbon dioxide sequestration into biomineral armor by ants

Over geologic time, Earths climate has been shaped by the capture and conversion of atmospheric carbon dioxide (CO2) into stable carbonate minerals, including dolomite [CaMg(CO3)2]. Accelerating natural carbon mineralization offers significant potential for mitigating anthropogenic climate change. Using stable carbon isotope tracking, nano-scale secondary ion mass spectroscopy, and 13C SSNMR, we show that, paralleling global biosphere-level processes, Sericomyrmex amabilis fungus-farming ants rapidly convert CO2 in their nest chambers into a biomineral layer covering their exoskeletons. We further reveal that biogenic carbon mineralization by these ants produces partially ordered dolomite. This rapid sequestration of CO2 into defensive armor in ants provides a fascinating natural example of mediation of potentially toxic accumulation of atmospheric CO2 that could inform human efforts to mitigate climate change.

ecology↗

bioRxiv2026

Progranulin deficiency induces lipid droplet accumulation in microglia via a STAT3-GPAT3 axis

Heterozygous mutations in the progranulin (PGRN) encoding gene GRN cause frontotemporal dementia (FTD), whereas homozygous GRN mutations lead to neuronal ceroid lipofuscinosis (NCL). However, the mechanisms underlying neurodegeneration due to PGRN deficiency remain unclear. In the aged brains or under neurodegenerative conditions, the accumulation of lipid droplets (LDs) in microglia contributes to cellular dysfunction and pro-inflammatory responses, exacerbating neurodegenerative pathology. Here, we investigated how PGRN deficiency induces LD accumulation in microglia. We found that PGRN ablation significantly upregulated triglycerol-3-phosphate acyltransferase 3 (GPAT3), the first and rate-limiting enzyme for triacylglycerol biosynthesis, and increased LD formation in both Grn-/- BV2 microglial cells and Grn-/-mouse brains. Mechanistic study revealed that PGRN deficiency upregulates GPAT3 via stimulating signal transduction and activator of transcription factor 3 (STAT3) signaling. Silencing Gpat3, inhibiting GPAT3 activity with the small molecule inhibitor FSG67, or PGRN restoration reduced LD accumulation and rescued the cytotoxicity of Grn-/- microglia conditional medium (MCM) toward N2a cells. Notably, intraperitoneal administration of FSG67 or AAV-MG1.2-mCx3cr1-mGrn-eGFP-mediated microglia-specific gene therapy reduced microglial LDs and ameliorated behavior phenotypes in Grn-/- mice. Our study elucidates the role of PGRN loss in microglial lipid homeostasis and identifies the STAT3-GPAT3 axis as a potential therapeutic target for LD-associated neurodegenerative diseases.

neuroscience↗

bioRxiv2026

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↗

bioRxiv2026

Unifying constraints linking protein folding and native dynamics decoded from AlphaFold

The interplay between protein folding and native dynamics remains a central question in biophysics. Analyzing an extensive set of AlphaFold-predicted structures, we uncover a robust relationship between folding topology (contact order) and native dynamics (fluctuation entropy), showing that long-range contacts that slow folding also restrict conformational flexibility across protein sizes and taxonomic groups. Scaling analysis reveals that this relationship, together with its chain-length dependence, is consistent with power-law-like trends, reflecting common organizing constraints of protein architecture. Across species, increasing organismal complexity is associated with proteome-wide shifts toward lower contact order and higher fluctuation entropy. Together, evidence from folding, stability, and functional dynamics converges on unifying constraints, revealing an intrinsic physical organizing principle captured by AI models.

bioinformatics↗

bioRxiv2026

Love-thy-neighbor: Neural networks for tracking and lineage tracing in budding yeast

Tracking and lineage tracing are widely needed tasks in biological image analysis. For cells that grow and divide, tracking is challenging because cells change in number, shape, and size throughout a recording. As the time interval between images increases, it becomes more difficult to establish correspondences between cells across timepoints. Consequently, tracking has to be performed between consecutive or temporally close images, which leads to exponentially decreasing tracking accuracy and thus high sensitivity to error rates. For budding yeast, this challenge is further heightened by the similarity of cells in colonies, their dense packing, the asymmetric nature of cell divisions, and movement due to growth of the colony. A related task, lineage tracing, is similarly challenging without fluorescent markers due to multiple potential mother cells surrounding a new daughter cell. Here, we present neural networks for budding yeast tracking and lineage tracing, named LYN-track and LYN-trace, respectively. These methods leverage fine geometric features of cells and their neighborhoods. To train and test the algorithms, we recorded and annotated new budding and fission yeast microscopy movies (78,852 frame-to-frame tracklets, 2,512 images), which we make freely available. On these and existing datasets, our neural network-based methods demonstrate robust, above state-of-the-art performance. Both tools have been integrated into graphical user interfaces (GUIs), available on Github, and can be straightforwardly retrained with custom data if desired.

bioinformatics↗

bioRxiv2026

A mediterranean-mimicking diet harnesses gut microbiota-derived 3-IAA to rejuvenate T cell

Diet profoundly shapes the tumor microenvironment through metabolite modulation, yet the mechanisms linking diet, gut microbiota, and antitumor immunity remain unclear. Here, we demonstrate that a mediterranean-mimicking diet (MedDiet) suppresses tumor growth by orchestrating a microbiota-metabolite-immune axis. MedDiet selectively enriched Bacteroides thetaiotaomicron (B. thetaiotaomicron) in the gut, whose administration recapitulated tumor suppression. Both MedDiet and B. thetaiotaomicron elevated plasma levels of the tryptophan metabolite indole-3-acetic acid (3-IAA). Mechanistically, 3-IAA enhanced CD8+ T cell cytotoxicity and alleviated exhaustion by inhibiting the integrated stress response, sustaining antitumor immunity in vivo. Importantly, 3-IAA synergized with anti-PD-1 therapy to further restrain tumor progression. Finally, we developed a MedDiet Score to predict patient survival and response to immunotherapy. These findings reveal that dietary modulation of gut microbiota can reshape systemic metabolites to potentiate T cell-mediated antitumor responses. Our study identifies 3-IAA as a metabolite-based adjuvant for immune checkpoint therapy and highlights the translational potential of diet-driven immunomodulation in cancer treatment.

cancer biology↗

bioRxiv2026

A comprehensive analysis of flagellar mutations in Vibrio cholerae: Trade-off mechanisms between motility loss and host adaptability

IntroductionCholera, caused by Vibrio cholerae, is a severe diarrheal disease threatening global health. The flagellum of V. cholerae functions not only for motility but also as an environmental sensor regulating virulence. The trade-off mechanism between motility loss and enhanced host adaptation remains unclear. ObjectiveThis study aimed to elucidate how flagellar mutations, which lead to a loss of motility, affect host adaptability in V. cholerae and to uncover the underlying molecular basis. MethodsWe analyzed 3,135 cholera-related samples to identify mutation hotspots in flagellar genes. A relevant flagellar mutant library was constructed and assessed for host adaptability. Multiple approaches, including molecular, genetic, transcriptomic, and proteomic analyses, were applied to dissect the FlgM-mediated pathway, with key findings revalidated in an adult mouse model using a specifically constructed 6N-labeled mutant pool. ResultsBig data analysis reveals those flagellar mutations in V. cholerae cluster in key structural and regulatory genes, including flhB, fliA, fliF, fliD, and fliM. Flagellar mutations led to a scenario where the secretion level of the regulator FlgM was negatively correlated with host adaptability. Intracellular FlgM inactivates either the {sigma}28 factor FliA directly or acts through the VarS/VarA-CsrA/BCD system, ultimately leading to the derepression of the quorum-sensing master regulator named hapR. HapR can directly bind to the promoters of genes involving in methionine transportation to regulate adaptability of V. cholerae. The 6N-labeled mutants pool experiment reconfirmed that motility loss promotes host adaptability via the FlgM-FliA-HapR-methionine axis. ConclusionOur findings demonstrate that secretion levels of the flagellar regulator FlgM drive an adaptive shift in V. cholerae from motility to host adaptability, mediated through quorum sensing and methionine metabolic reprogramming. This reveals a novel mechanism underlying bacterial evolution and pathogenicity.

microbiology↗

bioRxiv2026

Multitimescale Computation by Astrocytes

The basic computational unit of the brain has long been defined as the neuron. However, mounting evidence suggests that other cells, especially astrocytes, also perform computations. Here, we demonstrate that cerebellar astrocytes decompose norepinephrine input into slow and fast calcium ion activities through differential adrenergic receptor engagement. During reward learning in mice, these slow and fast activities selectively target and modulate distinct synaptic pathways. Causal manipulations reveal that fast 2-adrenergic signals govern event-triggered responses and reinforcement learning, whereas slow 1-adrenergic signals maintain behavioral states and coordinate transitions. Remarkably, an actor-critic neural network trained on a similar sequence task spontaneously recapitulates these multitemporal dynamics, suggesting that astrocytes implement critic-like computations that evaluate states and modulate neuronal learning. These findings establish astrocytes as multilevel processors that transform univariate neuromodulatory inputs into multivariate, pathway-specific circuit controls operating in parallel with neuronal processing.

neuroscience↗

bioRxiv2025

The Hippo Pathway Regulates Corneal Endothelial Regeneration

Corneal endothelial cells (CECs) have limited regeneration capacity in primates while display a potent restorative capability in some species such as rodents after wounding. The mechanism which determines the regenerative capability of CECs remains poorly understood. Here, we identify that the Hippo signaling pathway is inhibited and the downstream effector YAP is activated during CEC wound healing in rabbit and mouse. Knockdown of Yap1 and pharmacological inhibition of YAP suppresses CECs wound healing in rodents in both in vitro and in vivo models. XMU-MP-1, a specific small molecular inhibitor for Hippo signaling pathway, can promote the corneal endothelial regeneration in rodents and corneal endothelial proliferation in cultured primate CECs, as well as in vivo non-human primate CEC wounding model. These findings suggest that Hippo pathway serves as a conserved signal to regulate corneal endothelial regeneration among various species, providing a novel target for non-invasive treatment of corneal endothelium decompensation.

cell biology↗

bioRxiv2025

A convergent cortical scheme for visual scene segmentation

Scene segmentation, a key step towards structured understanding of natural environments, entails a complementary set of computations. Instead of accessing these segmentation computations in isolation, we perceive the segregated object as a unified whole, but the neural basis supporting such a unitary percept remains unclear. We bridged this gap by showing a convergent coding scheme: an object-level additive code in the primary visual cortex, which serves as a spatial segmentation mask for the object. Across individual neurons, this code uniformly boosted their responses to the segmented object. In the population space, this code created an orthogonal representational geometry by perpendicularly displacing the neural manifold for image features, efficiently multiplexing both local and global information about the object. Computational modeling further revealed the utility and optimality of this convergent coding scheme, which effectively isolates objects in cluttered environments and in turn unclutters downstream object representations. Our findings reveal the computational logic of visual segmentation and call for a revision of the visual cortical hierarchy.

neuroscience↗

bioRxiv2025

Evolutionary persistence and divergence of the tdk killer meiotic driver family

Killer meiotic drivers (KMDs) are selfish genetic elements that achieve super-Mendelian inheritance by selectively eliminating gametes lacking the driver. Although predicted to arise recurrently, KMDs are generally considered evolutionarily ephemeral--going extinct after fixation or host suppression. The identification of tdk1, a single-gene KMD in the fission yeast Schizosaccharomyces pombe, provides a model for studying KMD evolution. Here, we identify two divergent tdk1 homologs (tdk210 and tdk203) from S. cryophilus, a fission yeast species that diverged [~]100 million years ago from S. pombe, as active KMDs. These three KMDs all act via post-germination killing, disrupting chromosome segregation in noncarrier progeny. Notably, they also exhibit striking functional divergences: tdk1, tdk210, and tdk203 are mutually incompatible (showing no cross-resistance), and the latter two act independently of Bdf1/Bdf2--host chromatin proteins required for tdk1 killing. Phylogenetic analyses of the dozens of tdk family genes in Schizosaccharomyces support long-term persistence and rapid evolutionary dynamics of this gene family. Remarkably, homologs in distantly related fungal phyla display genomic and structural similarities to Schizosaccharomyces tdk genes, suggesting a deeply rooted origin of this KMD family in fungi. Our findings reveal that a single KMD family can undergo repeated functional innovation--generating mutually incompatible variants and rewiring host dependencies--while maintaining a conserved killing mode over deep evolutionary time.

evolutionary biology↗

bioRxiv2025

Structural Insights into Single-Stranded DNA Recognition and Modified Substrate Tolerance in an Engineered Terminal Deoxynucleotidyl Transferase

Terminal deoxynucleotidyl transferase (TdT) is the cornerstone enzyme for de novo enzymatic DNA synthesis (EDS), promising to overcome the length and sustainability limitations of traditional phosphoramidite chemistry. We previously identified a highly active TdT ortholog from Zonotrichia albicollis (ZaTdT) and engineered a variant (R335L/K337G) capable of efficiently incorporating 3-aminooxy (3-ONH2) reversible terminators. However, the atomic-level mechanism by which these engineered mutations alter substrate specificity has remained elusive. Here, we present the high-resolution (2.20 [A]) crystal structure of the engineered ZaTdT in complex with a single-stranded DNA primer. Structural analysis reveals a conserved catalytic core anchored by a hydrophobic platform (Phe110/Phe257/Trp308) that stabilizes the primer. Crucially, comparative modeling with the homologous murine TdT ternary complex demonstrates that the engineered mutations (corresponding to L190/G192 in the crystal structure) disrupt a rigid salt-bridge network at the active site entrance. This electrostatic remodeling not only reduces local positive charge but also expands the catalytic pocket depth from 3.8 [A] to 5.8 [A]. This specific spatial expansion provides the structural rationale for the accommodation of bulky 3-blocking groups, validating our rational design strategy and paving the way for next-generation long-read DNA synthesis.

biochemistry↗

bioRxiv2025

A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

Genetics studies have identified a core set of regulators essential for pancreatic {beta} cell development, many of which are mutated in monogenic diabetes. However, how these mutations alter developmental trajectories to produce pathological cell states remains elusive. Here we introduce a knockout village framework that enables longitudinal scRNA-seq profiling of 79 human pluripotent stem cell mutant lines targeting 30 developmental regulators, including 15 diabetes genes, across five islet differentiation stages. We show that loss of lineage regulators impairs {beta} cell formation in a stage-specific manner and rewires developmental trajectories towards competing lineages. Notably, several monogenic diabetes gene mutations drive a shift from {beta} cells to enterochromaffin (EC)-like cells, a recently recognized non-canonical islet cell fate. These EC-like cells exhibit incomplete activation of hormone regulation programs, along with elevated neuron signatures. Leveraging the diversity of cell fate outcomes across mutants, we predicted and experimentally validated ISL1 as a key downstream effector of PDX1 and PAX6 that safeguards {beta} cell identity against an EC-like fate. Together, our findings reveal cell fate rewiring as a widespread, previously underappreciated pathological mechanism in monogenic diabetes and establish a scalable platform for uncovering developmental vulnerabilities in human genetic disorders.

developmental biology↗