Biology subjects

Choi, Y.

Publications and source records attributed to Choi, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Structure-guided deimmunisation of Fel d 1 suppresses allergic effector functions ex vivo

Allergic responses to the major cat allergen Fel d 1 are primarily driven by immunoglobulin E (IgE) cross-linking on effector cells. While conventional allergen-specific immunotherapies often rely on whole-allergen extracts with inherent risks of systemic reactions, rationally engineered variants offer a safer path to desensitisation. We present a structure-guided strategy to deimmunise Fel d 1 by selectively disrupting crucial IgE-binding interfaces. Using a computational pipeline integrating structural mapping and immunoinformatics, we designed 30 single-point mutations targeting immunodominant regions. Ex vivo functional evaluation using sera from cat-allergic individuals demonstrated that specific variants, notably K29G in Chain 1, exhibited significantly diminished IgE reactivity and profoundly suppressed basophil activation. Furthermore, CRISPR/Cas9-mediated introduction of the K29G mutation into feline fibroblasts confirmed that the substitution preserves fundamental cellular proliferation. This work demonstrates that targeted computational design can not only yield superior candidates for safer immunotherapeutics but also establish a viable foundation for generating genetically edited, hypoallergenic cats.

immunology↗

bioRxiv2026

Fluorescent organelle markers in Cryptococcus neoformans: a versatile toolkit for live-cell subcellular localization

Understanding how intracellular organelles are organized and dynamically remodeled is essential for elucidating fungal growth, differentiation, and pathogenicity. The human fungal pathogen Cryptococcus neoformans exhibits remarkable morphological diversity, yet the contribution of intracellular organelles to adaptation across environmental and host-relevant conditions has not been systematically examined. Here, we establish a comprehensive toolkit of fluorescent organelle marker plasmids and strains expressing mCherry or GFP fusions, enabling high-resolution live-cell imaging of ten major subcellular compartments: the nucleolus, endoplasmic reticulum (ER), Golgi apparatus, mitochondria, peroxisome, endosome, autophagosome, vacuole, the plasma membrane, and processing bodies (P-bodies). With this platform, we analyzed organelle organization under host-relevant conditions, including elevated temperature, 5% CO2, and capsule- and melanin-inducing media, as well as throughout sexual development from zygote formation to basidiospore production. We further show that the toolkit supports colocalization analyses via diploid formation or dual-labeling strategies. Collectively, our results reveal condition- and stage-specific remodeling of organelle architecture during vegetative growth and mating. This imaging platform provides a robust framework for investigating how subcellular organization supports fungal adaptation, development, and virulence, and for inferring the functions of uncharacterized genes from their spatial localization.

cell biology↗

bioRxiv2026

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome

The gut microbiome regulates many aspects of human biology, including immunity and inflammatory diseases, yet mechanistic discovery and translation remain constrained by fragmented workflows and manual hypothesis integration. Here, we present Eubiota, an open-source modular agentic framework that decomposes microbiome inquiry using specialized agents for planning, execution, verification, and grounded synthesis. Coordinated through shared memory and domain-specific tools, Eubiota employs reinforcement learning to optimize multi-turn reasoning, achieving 87.7% benchmark accuracy and outperforming GPT-5.1 by 10.4%. Across four case studies, Eubiota enabled end-to-end discovery with experimental validation. Screening nearly 2,000 bacterial genes, Eubiota identified the uvr-ruv DNA repair axis as a fitness determinant under inflammatory stress, validated using transposon mutants and IBD metagenomes. It further designed a four-strain consortium that attenuated colitis severity in mice and generated a commensal-sparing antibiotic cocktail, demonstrating its utility in addressing community-level design challenges at cellular and molecular levels. Finally, Eubiota discovered diet-associated metabolites that suppress NF-{kappa}B signaling. Together, these results establish Eubiota as a scalable, tool-grounded scientific copilot for mechanistically driven microbiome discovery.

bioinformatics↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2026

Systems-level phosphoproteomics reveals conserved and subunit-specific STRIPAK signaling networks in Cryptococcus neoformans

The striatin-interacting phosphatase and kinase (STRIPAK) complex is a conserved PP2A-associated signaling hub that integrates kinase-phosphatase networks, yet its roles in human fungal pathogens remain poorly defined. Here, we dissected STRIPAK functions in the opportunistic pathogen Cryptococcus neoformans by combining genetic, genomic, virulence, and phosphoproteomic analyses across mutants lacking individual STRIPAK subunits. Loss of the core STRIPAK components via PPH22, FAR8, FAR9, or FAR11 mutations caused severe defects in growth, stress adaptation, cell-cycle progression, and morphogenesis, accompanied by widespread aneuploidy and genome instability. In murine infection models, far11{Delta} strains were avirulent, whereas far9{Delta} mutants caused delayed but ultimately fatal disease and underwent host-associated genome remodeling, with recovered isolates exhibiting chromosome 11 amplification despite no consistent in vitro fitness advantage. In contrast, deletion of MOB3 produced a hypervirulent phenotype. mob3{Delta} cells exhibited enhanced transmigration across an in vitro blood-brain barrier model, increased survival in macrophages, and generated small-cell morphotypes, features associated with increased dissemination. Phosphoproteomic profiling revealed extensive and overlapping phosphorylation changes among core STRIPAK mutants, affecting pathways involved in signaling, cytoskeletal and cell-cycle control, chromatin regulation, RNA metabolism, and stress responses. Conversely, mob3{Delta} mutants displayed a smaller, largely distinct phosphoproteomic signature. Network and functional enrichment analyses highlighted STRIPAK-dependent regulation of TORC2-associated signaling, MAPK/GTPase signaling, autophagy, nuclear transport, RNA processing, DNA replication, and ribosome biogenesis. Together, these findings establish STRIPAK as a coordinator of genome stability, morphological plasticity, stress adaptation, and virulence in C. neoformans, and demonstrate that individual STRIPAK subunits drive shared yet divergent signaling outputs that shape host-pathogen interactions. ImportanceFungal pathogens must rapidly adapt their growth, morphology, and stress responses to survive within the host, requiring precise coordination of cellular signaling pathways. The conserved striatin-interacting phosphatase and kinase (STRIPAK) complex controls key developmental programs in eukaryotes, but its roles in fungal pathogenesis are not fully defined. We previously showed that STRIPAK is important for genome stability, development, and virulence in the opportunistic human fungal pathogen Cryptococcus neoformans. Here, we define how individual STRIPAK subunits differentially regulate fungal morphogenesis, genome plasticity, host adaptation, and virulence, revealing both shared and subunit-specific functions within this conserved signaling complex. Core STRIPAK mutants exhibit severe growth and stress-response defects and attenuation of virulence, whereas loss of the Mob3 subunit promotes hypervirulence by enhancing dissemination and persistence within the host. Phosphoproteomic profiling reveals that individual STRIPAK components exert shared yet distinct control over phosphorylation networks that shape host-pathogen interactions, establishing STRIPAK as a central signaling hub and a potential target for antifungal intervention.

microbiology↗

bioRxiv2025

Effects of human stress on horse behavior and interaction quality

Human-horse interaction can be influenced by the emotional and physiological state of humans, as horses are highly sensitive to human stress. Understanding these effects is essential for improving outcomes in equine-assisted activities. This study examined how human stress impacts horse behavior and interaction quality. Seven humans and seven horses participated in a crossover design experiment in which participants viewed either stressful or relaxed video stimuli prior to interacting with horses. Electroencephalography (EEG), heart rate variability (HRV), and salivary cortisol was collected to assess human physiological responses, while the Human-Animal Interaction Scale (HAIS) and an ethogram evaluated interaction quality and horse behaviors. Stressful stimuli significantly increased beta and high-beta activity and altered HRV indices, indicated by increased low-frequency power and decreased high-frequency power. HAIS scores were lower under stress conditions, reflecting reduced interaction quality. Horses exhibited more pushing behavior and less lip-licking when handlers were stressed, although task completion time did not differ between conditions. These results demonstrated that human stress negatively influences both physiological states and behavioral outcomes within human-horse interactions. Therefore, managing emotional states and stress levels may enhance interaction quality and effectiveness in equine-assisted programs.

animal behavior and cognition↗

bioRxiv2025

Telomere-to-Telomere Accurate and Gapless Korean Standard Reference Genome

We present KOREF1-G-TTAGGA, the first Telomere-to-Telomere Accurate and Gapless Genome Assembly, standing as the Korean standard reference genome. The paternal and maternal haplotypes spanned 2.91 and 3.03 Gb. Genome-wide, at least 99.15% of assembled sequences were reliably haplotype-resolved, and over 95% remained accurate even in the most error-prone loci, including centromeric satellite arrays and segmental duplications. Rare-k-mer copy-number concordance within satellite arrays held up 98.9% and 98.8% per haplotype. Bionano optical maps fully spanned all canonical rDNA arrays on the five acrocentric chromosomes. The assembly quality index (AQI) of 99.77 and 99.69 exceeded the reference-quality threshold of 90, and more than 99.99% of gene and cCRE sequence was free of structural error. Both haplotypes further showed high base-level accuracy, with consensus quality value (QV) of 81.19 and 79.03, corresponding to one error per 131 and 80 Mb. KOREF1-G-TTAGGA is among the highest-quality East Asian telomere-to-telomere assemblies. It moreover anchors a decade-spanning multi-ome reference dataset for defining individual molecular states. Together, these resources define the personal referenceome as a foundation for individual biology and precision medicine, with the assemblies, annotations, and all multi-omic data openly available at https://koreanreference.org.

genomics↗

bioRxiv2025

Allosteric deimmunisation of a Salmonella phosphatase enhances catalytic function

Genetically engineered Salmonella strains are promising vectors for cancer therapy, but their clinical use is limited by host immune responses. A key immunogenic antigen, the phosphatase PhoN, is metabolically essential for bacterial survival in the vitamin B6-depleted tumour microenvironment and thus cannot be simply deleted. While conventional deimmunisation targets surface residues, we present a strategy of allosteric deimmunisation by mutating non-surface, buried residues within the dominant h2 helix T-cell epitope. We hypothesised that the epitope is allosterically coupled to the distal active site gate, allowing for the simultaneous modulation of immunogenicity and enzymatic function. Using a computational pipeline, we designed deimmunised variants and used molecular dynamics (MD) simulations to predict their functional effects. The simulations revealed that mutations in the h2 helix allosterically controlled the gates flexibility. The enzymatic activities of the deimmunized variants were correlated with the MD predictions: two of the five designed variants exhibited 2[~]3-fold increases in catalytic function. This work demonstrates that non-surface epitopes can be rationally engineered to not only ablate immunogenicity but also to allosterically enhance protein function.

biophysics↗

bioRxiv2025

10,239 whole genomes with multiomic and clinical health information as the Korean population multiomic reference dataset

We present Korea10K, the largest genomic dataset of the Korean population, comprising 10,239 high-coverage whole genomes (mean depth 30x) with matched multiomic profiles and phenotype data. Korea10K achieves complete and near-complete discovery of very rare and ultra-rare alleles, respectively, at 9,000 Korean genomes. This dataset provides the high-quality population-specific imputation panel, enabling accurate inference of low-frequency variants. Admixture analyses confirm the genetic homogeneity of the Korean population, despite its diverse Y-chromosomal, mitochondrial, and HLA repertoires. This pattern reflects a long and continuous lineage history characterized by persistent internal admixture and genomic homogenization over thousands of years on the Korean peninsula. We also identified 16.8 million genomic variants that directly modify CG sites by creating or abolishing CG dinucleotides, providing the population-scale evidence of coordinated genomic-epigenomic regulatory mechanism in Koreans.

genomics↗

bioRxiv2025

A deep reinforcement learning platform for antibiotic discovery

Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep-learning framework for de novo design of antibiotics that couples a 6.4-billion-parameter protein language model with reinforcement learning. The model is first fine-tuned on curated peptide data to capture antimicrobial sequence regularities, then optimised with proximal policy optimization against a composite reward that combines predictions from a learned minimum inhibitory concentration (MIC) classifier with differentiable physicochemical objectives. In vitro evaluation of 100 designed peptides showed low MIC values (nanomolar range in some cases) for all candidates (100% hit rate). Moreover, 99 our of 100 compounds exhibited broad-spectrum antimicrobial activity against at least two clinically relevant bacteria. The lead molecules killed bacteria primarily by potently targeting the cytoplasmic membrane. By unifying generation, scoring and multi-objective optimization with deep reinforcement learning in a single pipeline, our approach rapidly produces diverse, potent candidates, offering a scalable route to peptide antibiotics and a platform for iterative steering toward potency and developability within hours.

molecular biology↗

bioRxiv2025

STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features

The adaptive immune system monitors cellular integrity by recognizing short peptides from intracellular proteins presented on Major Histocompatibility Complex class I (MHC-I) molecules, collectively termed peptide-MHC complexes (pMHC), enabling detection of foreign or mutated proteins. With the rising importance of immunotherapies targeting neoantigens in cancers, the ability to accurately predict which peptides will bind to the diverse population of MHC alleles is critically important. Current computational methods for pMHC-I prediction fall broadly into sequence-based methods, which rely heavily on large training datasets, and structure-based methods that leverage structural modeling and energetics of pMHC binding. While sequence-based methods have been popularly used, their performance is dependent on the size and quality of training data. On the other hands, while structure-based approaches can generalize better across diverse MHC alleles, they traditionally depend on identifying a single global minimum energy conformation, an assumption that often fails due to the inherent binding promiscuity of MHC-I molecules. To address these limitations, we developed a STRUMP-I (STRUcture-based pMHC Prediction (for class I)), a novel pMHC binding prediction tool that directly leverages a broad set of force-field-derived energy terms as machine-learning features. STRUMP-I achieves performance comparable to state-of-the-art sequence-based models while significantly outperforming them on MHC alleles with limited representation in training data. Furthermore, STRUMP-I demonstrates strong synergy when integrated with sequence-based methods, notably enhancing prediction precision. The robustness and generalizability of STRUMP-I were confirmed by evaluating its predictive performance on independent, previously unseen datasets, including an experimentally validated cancer neoantigen dataset. This combined approach advances our capability to reliably identify clinically relevant neoantigen targets. The source code and trained models are available at https://github.com/yoonjoolab/STRUMP-I

bioinformatics↗

bioRxiv2025

cPLA2α Targeting to Exosomes Connects Nuclear Deformation to LTB4-Signaling During Neutrophil Chemotaxis

Efficient neutrophil chemotaxis requires the integration of mechanical forces and lipid-mediated signaling. While the signaling lipid leukotriene B4 (LTB4) reinforces cellular polarity, how mechanical cues regulate its production remains unclear. We now show that cytosolic phospholipase A2 (cPLA2), which is essential for the synthesis of LTB4, functions as a nuclear curvosensor. cPLA2 responds to nuclear constrictions by localizing to ceramide-rich inner nuclear membrane microdomains and incorporating onto the exofacial surface of nuclear envelope-derived exosomes. This unique topology enables localized LTB4 synthesis, which promotes myosin light chain II phosphorylation, and sustains polarity and directional persistence after constriction. In neutrophils squeezing through small constrictions, loss of cPLA2 impairs nuclear curvature sensing, exosomal LTB4 production, and post-constriction motility. These findings uncover a cPLA2-dependent mechano-chemical axis linking nuclear architecture to chemotactic efficiency and offering new strategies to modulate inflammatory responses.

cell biology↗

bioRxiv2025

Untargeted Plasma Metabolomics in Canine Cognitive Dysfunction: The Naturally Occurring Alzheimer's Disease Analog in Dogs

IntroductionCanine Cognitive Dysfunction (CCD) is an increasingly prevalent naturally occurring neurodegenerative condition in senescent dogs that share neuropathological and clinical features with human Alzheimers disease (AD). Metabolic profiling allows for identification of new candidates for AD biomarkers, diagnostics, and therapeutics. Despite its translational potential, plasma metabolomic profiling of dogs with CDD has not been previously characterized. MethodsThis case-control study analyzed plasma samples from ten client-owned geriatric dogs, including five with severe CCD and five age-matched, clinically healthy controls. Untargeted plasma metabolomics was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Multivariate and univariate statistical analyses identified significant metabolic differences between the groups. Metabolites were considered significant based on a variable importance in projection (VIP) score > 1.5, fold change (FC) > 2.0, and adjusted p-value < 0.05. ResultsFifteen metabolites across seven chemical classes were significantly altered in CCD dogs compared to controls, including glycerophospholipids, steroid derivatives, indoles, and mitochondrial-related compounds. Notably, elevated lysophosphatidic acid (LPA 20:2/0:0) and reduced ubiquinone-2 levels suggest dysregulation in neuroinflammatory and oxidative stress pathways. Cholesterol exhibited the highest FC and VIP scores, further reinforcing its role in AD pathogenesis. Hierarchical clustering and pathway enrichment analyses supported distinct metabolic signatures in CCD that mirror those observed in human AD. DiscussionThis is the first untargeted plasma metabolomic profiling of dogs with CCD, revealing systemic metabolic disturbances that align with AD pathophysiology. Data was collected from senescent community-dwelling companion dogs, which enhances the studys ecological and translational relevance. It supports the utility of CCD as an AD model and highlight candidate plasma biomarkers that warrant further investigation. Future longitudinal studies integrating metabolomics with neuroimaging, histopathology, and behavioral assessments are required to validate these findings and contribute to AD biomarker discovery and therapeutic development.

neuroscience↗

bioRxiv2025

γ-Amino Carboxylic Acid Modification Enhances the Efficacy of PNAs Targeting miR-221-3p in A549 Cells

Peptide nucleic acids (PNAs) are versatile tools for diagnostic and therapeutic applications, including gene regulation and miRNA targeting. However, their therapeutic potential is often limited by challenges such as biological efficacy. To address this, PNAs offer a key advantage over other nucleic acids--their ease of modification, which allows for enhanced properties. In this study, we introduced a novel{gamma} -amino carboxylic acid ({gamma}-ACA) modification to PNAs targeting miR-221-3p, a key miRNA implicated in various pathological processes. The modified PNAs showed significantly improved binding affinity to their targets and more efficient inhibition of miR-221-3p expression compared to unmodified PNAs in A549 cells, leading to effective regulation of downstream gene and protein expression. These results highlight the potential of{gamma} -modified PNAs as a platform for developing miRNA-targeted therapeutics.

molecular biology↗

bioRxiv2025

CPT1B-Mediated Fatty Acid Oxidation Induces Pigmentation in Solar Lentigo

IntroductionCellular senescence is associated with altered lipid metabolism, including increased cellular lipid uptake, upregulated lipid biosynthesis, and deregulated lipid breakdown. Previous studies have reported that carnitine palmitoyltransferase (CPT), the rate-limiting enzyme in fatty acid oxidation that catalyzes the conversion of acyl-CoA to acylcarnitine, is involved in various senescence-related diseases. Although solar lentigo (SL) is an age-related pigmentary disorder characterized by the accumulation of senescent cells, its role in metabolic dysregulation has rarely been investigated. Methods and ResultsIntegrated transcriptomic profiling of SL skin samples, combining mRNA sequencing, differential gene expression, pathway enrichment analyses, metabolic flux simulations, and protein-protein interaction analysis, was conducted to demonstrate the molecular alterations in SL compared to perilesional normal skin. We found transcriptomic alterations in mitochondrial energy metabolism-associated genes. Metabolic flux simulations revealed that carnitine-associated reactions involved in fatty acid oxidation were upregulated. Using a multi-omics approach, CPT1B was selected as a potential marker for SL, which was confirmed via its overexpression in immunohistochemical studies. Using a zebrafish model, CPT1B was implicated in melanogenesis. DiscussionCPT1B-mediated metabolic alteration is a key driver of SL pathogenesis. Targeting CPT1B and the associated lipid metabolism pathways is a novel therapeutic approach for managing SL and age-related pigmentation disorders. Research HighlightsSolar lentigo (SL) exhibits altered mitochondrial metabolism and fatty acid oxidation. CPT1B activation regulates pigmentation, suggesting that targeting CPT1B may offer a novel therapy for SL and other age-related pigmentary disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/659823v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@81fce3org.highwire.dtl.DTLVardef@1bf3forg.highwire.dtl.DTLVardef@b2c119org.highwire.dtl.DTLVardef@1a38b23_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Changes in biophysical characteristics of YghA from E. coli due to variation in pH

YghA from E. coli has been reported to be involved in conferring tolerance against furan aldehyde inhibitors which are commonly generated in thermo-acidic pretreatment of lignocellulosic biomass. In this study we report the biophysical characterization of YghA from E. coli as a function of variation in pH. Fluorescence intensity of YghA increased by 2.5-fold in acidic pH as compared to circumneutral pH. In presence of the hydrophilic 8-anilinonaphthalene-1-sulfonic acid (ANS) dye, a 68 - 79.4-fold increase in fluorescence intensity at acidic pH was observed as compared to circumneutral pH, while at basic pH the increase was only 1 to 2-fold. Secondary structure analysis by circular dichroism signal at 222 and 208 nm suggests that the secondary structure of YghA is primarily composed of alpha-helix at pH 7 and the secondary structure is abruptly lost at pH 3 and lower. In agreement with these observations, MD simulations predicted greater structural variations at low pH when compared to neutral or high pH. Interface energy calculations using computational docking protocols suggested that YghA forms relatively more stable complex with NADH. The in silico pulling assay results also show that NADH is more preferred compared to NADPH. Molecular dynamics simulations also indicate that YghA is structurally unstable at acidic pH with significant variations in the root mean square deviation values of the tetramer backbone. Residues GLU 84 at pH 7 together with PRO 24 and LEU 236 at pH 1 were identified as flexible residues and are promising target for future mutagenesis studies targeted towards improving structural stability of YghA.

biochemistry↗

bioRxiv2025

Unisexual reproduction in the global human fungal pathogen Cryptococcus neoformans

The human fungal pathogen Cryptococcus species complex (encompassing C. neoformans, C. deneoformans, and the C. gattii species complexes) exhibit diversity in sexual reproduction, including -a mating, pseudosexual reproduction, as well as unisexual reproduction initiated from a single isolate or between isolates of the same mating type. A central conundrum is that while most Cryptococcus natural populations exhibit significant mating-type bias, genetic and genomic analyses show recombination occurs in nature. The discovery of unisexual reproduction in C. deneoformans provided insight; however, thus far unisexual reproduction has never been directly observed in the predominant global pathogenic species C. neoformans. Here, we provide evidence that mutating the RIC8 gene, which encodes a conserved guanine nucleotide exchange factor (GEF) involved in both chaperoning and activating G proteins, enables unisexual reproduction in C. neoformans. Additionally, we show that genetic variation in the natural population promotes unisexual reproduction, and unisexual reproduction in C. neoformans involves canonical meiotic recombination. Finally, we found that deletion of both GPA2 and GPA3 in the MAT background leads to self-filamentation without sporulation, suggesting that differential modulation of the G proteins, likely involving Ric8, could underlie the switch between different modes of sexual reproduction in Cryptococcus. Our study further highlights that the highly conserved Ric8 GEF can act as an important regulator of cellular development in response to environmental stimuli and could modulate sexual reproduction in nature. We hypothesize that unisexual reproduction occurs much more frequently in nature than currently appreciated, and possibly in other fungi and microbial eukaryotes as well. Significance statementSexual reproduction is a central tenet of the eukaryotic life cycle, essential for the long-term survival of a species by promoting genetic diversity and facilitating natural selection. In eukaryotes such as unicellular basidiomycetous fungi, sexual reproduction leads to hyphal growth and spore production, enabling escape from harsh environments and long-distance dispersal. Here, we report that mutating the RIC8 gene, encoding a conserved guanine nucleotide exchange factor (GEF) involved in activation of G proteins, enables unisexual reproduction in the predominant human fungal pathogen Cryptococcus neoformans that involves canonical meiosis. Our findings suggest that conditions might exist in nature that could induce, and even promote, unisexual reproduction in Cryptococcus, highlighting the complexity and importance of sexual reproduction in this prominent fungal pathogen.

genetics↗

bioRxiv2025

STRIPAK complex defects result in pseudosexual reproduction in Cryptococcus neoformans

STRIPAK is an evolutionarily conserved signaling complex that coordinates diverse cellular processes across fungi and animals. In the human fungal pathogen Cryptococcus neoformans, STRIPAK was recently shown to play critical roles in maintaining genome stability and controlling both sexual and asexual development. In Cryptococcus, sexual reproduction is closely linked to virulence, and our findings demonstrate that the STRIPAK complex plays key roles in both processes. Here, we further investigate the specific roles of the STRIPAK catalytic subunit Pph22 and its regulatory partner Far8 during sexual development. We show that while pph22{Delta} mutants are defective in -a sexual reproduction, exhibiting impaired meiotic progression and a failure to produce viable spores, the deletion of PPH22 resulted in exclusive pseudosexual reproduction, with progeny inheriting nuclear genomes solely from the wild-type parent. Overexpression of PPG1, a related phosphatase, rescued growth and developmental defects in pph22{Delta} mutants, and restored the preference for -a sexual reproduction over pseudosexual reproduction during mating, suggesting functional redundancy within the STRIPAK signaling network. Furthermore, deletion of FAR8, another component of the STRIPAK complex, also led to a high rate of pseudosexual reproduction during -a sexual mating, reinforcing the role of STRIPAK in modulating reproductive modes in C. neoformans, possibly through regulating nuclear inheritance and meiotic progression. Together, these findings highlight the distinct contributions of STRIPAK to sexual reproduction in C. neoformans and suggest that disruptions of this complex affect genome integrity and inheritance mechanisms, with broader implications for fungal adaptation and pathogenesis.

genetics↗