Biology subjects

Ma, W.

Publications and source records attributed to Ma, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Cell-type specific allelic dampening of sex-linked genes in sex chromosome aneuploidy

Common sex chromosome aneuploidies (SCAs) often present with cognitive and cardiovascular dysfunction in humans. To address SCA effects on gene expression and DNA methylation in relevant cell types, we differentiated neural precursor cells (NPCs) and cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) with different numbers of sex chromosomes, including isogenic and independent lines. As expected, the expression of genes that escape X inactivation (escapees) mostly increases with the number of inactive X chromosomes (Xi). However, allelic analysis shows dampening of escapees specifically on the Xi in XXY compared to XX in both NPCs and CMs, revealing a novel type of dosage compensation in SCA. In contrast, Y-linked gene expression is higher in XXY versus XY NPCs, but the opposite is observed in CMs. This may explain the greater number of differentially expressed autosomal genes in NPCs versus CMs with an added Y chromosome, while effects of added X chromosomes are similar between cell types. Concordantly, changes in autosomal DNA methylation are mainly driven by the presence of a Y chromosome. These findings highlight the cell-type specificity of sex-linked and autosomal gene regulation in SCA conditions. HighlightsO_LISex chromosome aneuploidy induces cell-type specific changes in gene expression C_LIO_LIDampening of the inactive X chromosome in XXY alleviate X overexpression C_LIO_LIHigh Y-linked gene expression in XXY neuronal precursor cells but not cardiomyocytes C_LIO_LISex chromosome aneuploidy disrupts sex biases in autosomal gene expression C_LI

molecular biology↗

bioRxiv2026

Protenix-v2: Broadening the Reach of Structure Prediction and Biomolecular Design

Advances in biomolecular modeling have broadened the range of problems addressable by structure prediction and design models. Here, we present results from Protenix-v2, a system spanning high-accuracy structure prediction and biomolecular design. On the structure prediction side, Protenix-v2 achieves antibody-antigen success rates with up to 13-point gains over Protenix-v1, while 5-seed performance surpasses previous 1000-seed results. On the design side, Protenix-v2 demonstrates a 100% target-level success rate in novelty-controlled VHH-Fc campaigns, reaching hit rates up to 48%. Crucially, the model enables hit discovery on difficult GPCR targets with hit rates of 16%-88% (VHH-Fc) and up to 50% (mAb) under 16-30 testing budgets per target. Resulting hits show high developability and diversity. Beyond antibody tasks, we report improved ligand-related plausibility and successful cross-variant SARS-CoV-2 spike RBD mini-binder design. These results establish Protenix-v2 as a robust and powerful model for accelerated drug discovery.

molecular biology↗

bioRxiv2026

A stage-resolved map of dynamic septin interactions required for infection by the rice blast fungus

Septin GTPases are essential cytoskeletal regulators that organize membranes and scaffold protein complexes to control cytokinesis, polarity, and morphogenesis. How septins execute these functions remains poorly understood, and comprehensive, stage-resolved interaction maps are lacking. Here, we define a quantitative, time-resolved septin interactome in the rice blast fungus Magnaporthe oryzae using immunoprecipitation coupled to mass spectrometry. We map more than 350 interactors of septins Sep3, Sep4, Sep5 and Sep6, revealing a dynamic network required for appressorium-mediated plant infection. Beyond canonical roles in cytoskeletal organisation and polarity, septins associate with proteins linked to membrane remodelling, metabolism, and virulence, deployed during host invasion. Integration with ultra-high-throughput yeast two-hybrid analysis defines a high-confidence septin interactome and identifies previously uncharacterised factors, including Msi1, a BAR domain protein required for invasive growth. Together, these findings establish septins as dynamic organisers of infection-related processes and provide a framework for understanding how cytoskeletal scaffolds coordinate fungal pathogenesis.

cell biology↗

bioRxiv2026

Myosin binding protein-C limits strain induced cross-bridge detachment in response to rapid stretch in cardiac and skeletal muscle

Myosin binding protein-C (MyBP-C) consists of a family of regulatory proteins expressed in sarcomeres of cardiac, fast and slow twitch skeletal muscles. The 3 MyBP-C paralogs expressed in each muscle type are encoded by separate genes but maintain a similar structure. Given the overall similarity in structure and localization of each of paralog, it is assumed that MyBP-C expressed in different muscles have similar functional effects. Here we directly tested this assumption by making use of our cut and paste approach to remove and replace N-terminal regions of MyBP-C in sarcomeres of different muscle types. We found that the different MyBP-C paralogs similarly slowed cross-bridge cycling kinetics, increased Ca2+ sensitivity of tension, and damped force oscillations. However, responses to a rapid stretch in actively contracting fibers, taken as indices of cross-bridge detachment and attachment kinetics, differed in each muscle type and responses depended on the presence or absence of a given paralog of MyBP-C. Altered responses to stretch were most evident for fast MyBP-C where loss of MyBP-C in psoas muscle resulted in transient responses to stretch that resembled those found in cardiomyocytes. Replacement of cardiac MyBP-C with fast MyBP-C in cardiomyocytes led to responses similar to psoas muscle. In separate X-ray diffraction experiments we also found that loss of MyBP-C in Ca2+-activated psoas muscle increased lattice disorder, reduced the ordering of myosin heads, and decreased thin filament length. Taken together, these results indicate that the different MyBP-C paralogs exert both common and unique effects on myosin cross-bridge kinetics. Significance StatementMyBP-C is a family of regulatory proteins found in muscle sarcomeres, where they regulate contraction and relaxation. Mutations in all MyBP-C paralogs cause disease in skeletal and cardiac muscles. We used a powerful "cut and paste" strategy to selectively remove MyBP-C from slow-twitch, fast-twitch, and cardiac muscle to show that each MyBP-C effects cross-bridge behavior similarly, though to varying degrees. Each MyBP-C had a notable effect on transient responses to rapid stretch, where MyBP-C was found to limit strain-induced cross-bridge detachment, especially in fast-twitch muscles. Strain-induced cross-bridge detachment is critical for rapid filling of the left ventricle in diastole and for sustained contraction in skeletal muscle. MyBP-C paralogs appear adapted to meet the mechanical demands of each muscle type.

physiology↗

bioRxiv2026

Effects of prolonged post-fixation on vascular biomarkers in postmortem human brains

Postmortem human brains stored in brain banks are important research resources to study the mechanisms underlying normal brain functions as well as various neurodegenerative disorders. Immunohistochemical (IHC) and histochemical (HC) staining have been used to examine human brains fixed in neutral-buffered formalin (NBF) for months, years, and even decades. As such, it is essential to establish the effects of prolonged fixation in NBF on both IHC and HC stains. Previously, we found that prolonged NBF fixation resulted in differential effects on IHC and HC staining on postmortem brains. In this study, we further examined the effects of prolonged fixation on IHC stains targeting 6 antigens and 2 HC stains of known biomarkers of cerebrovascular diseases in prefrontal cortex of human brains fixed for 1, 5, 10, 15, and 20 years. The IHC targets included microvasculature markers of the blood brain barrier (Collagen-IV and Claudin-5), a type III intermediate filament marker (Vimentin), an activated microglia marker (CD68), a biomarker for oligodendrocytic myelin proteolipid protein (PLP) and a marker for iron accumulation (Ferritin). The HC included Massons Trichrome Stain (MTS) and Bielschowsky silver stain (BSS). We found that staining intensities of Ferritin, Vimentin, Collagen-IV and BSS decreased with prolonged fixation, while no significant differences were observed in the staining intensity of other markers. Hence, these differential alterations should be taken into consideration when interpreting the results from processed tissues with prolonged fixation. We recommend performing IHC and HC staining for human brains with the same fixation times to offset any impact on downstream neuropathological analyses, as well as adding the fixation duration as a covariate in the analysis.

neuroscience↗

bioRxiv2026

A specialized ARGONAUTE enables trans-species RNA interference in plant immunity

Trans-species RNA interference (tsRNAi), in which plants produce small RNAs (sRNAs) to silence target genes in pathogens, has emerged as a promising strategy for disease control. However, whether tsRNAi constitutes an endogenous, regulated immune response remains unclear. Here, we show that ARGONAUTE10 (AGO10) plays a critical role in pathogen-induced tsRNAi. Loss of AGO10 in Arabidopsis abolished pathogen gene silencing during infection, leading to hypersusceptibility to oomycete and fungal pathogens. Importantly, AGO10 rapidly responds to pathogen infection through increased protein accumulation and re-location into discrete cytoplasmic condensates, thus promoting the production of trans-species sRNAs at the pathogen infection sites. This immune responsiveness relies on the N terminal intrinsically disordered region (IDR) of AGO10, which is responsible for sensing and responding to immune activation. Specific features in the IDR partitions AGO10 into two deeply diverged subgroups, AGO10a and AGO10b, with the immune responsiveness and defense function evolutionarily conserved in AGO10a but not AGO10b. Together, these findings establish tsRNAi as a bona fide, evolutionarily conserved immune response and position AGO10 as a signal-responsive hub linking pathogen perception to tsRNAi-based defense.

plant biology↗

bioRxiv2026

Protenix-v1: Toward High-Accuracy Open-Source Biomolecular Structure Prediction

We introduce Protenix-v1 (PX-v1), the first fully open-source structure prediction model to attain superior performance to AlphaFold3 while strictly adhering to the same training data cutoff, model size, and inference budget. Beyond standard evaluations, we highlight the effectiveness of inference-time scaling behavior of Protenix-v1, demonstrating that increasing the sampling budget yields consistent improvements in prediction quality--a behavior previously observed in AlphaFold3 and largely absent from prior open-source models. In addition to improved accuracy, Protenix-v1 incorporates key capabilities including protein template integration and RNA MSA support. Furthermore, to better support real-world applications such as drug discovery, we additionally release Protenix-v1-20250630, a variant trained on a larger dataset (cutoff: June 30, 2025), delivering further improved prediction accuracy. Finally, we identify limitations in existing benchmarking practices and provide updated evaluation tools and year-stratified benchmarks to support more reliable and transparent assessment. Collectively, these contributions provide a robust foundation for the Protenix series and the broader field.

bioinformatics↗

bioRxiv2026

A spatial-temporal atlas of human islet pathophysiology identifies a size-dependent trajectory from compensation to decompensation

Type 2 diabetes (T2D) is characterized by progressive islet dysfunction, yet the transition from functional adaptation to failure remains poorly defined within the native tissue architecture. Using multiplex imaging mass cytometry, we systematically analyzed human pancreatic islets across a spectrum of non-diabetic (ND), prediabetic (PreD), and T2D donors, revealing that pathological remodeling is profoundly size-dependent. This remodeling is manifested as a coordinated evolution of subpopulation abundance, endocrine cell proportions, structural integrity, and protein expression profiles, revealing that islets of different sizes undergo divergent fates during disease progression. We identified a size-dependent vulnerability spectrum where medium-and large-sized islets (>100 m in diameter) serve as the primary histopathological correlates of glycemic failure (HbA1c), exhibiting early density loss and structural disintegration. In contrast, small islets (30-100 {micro}m in diameter) exhibited compensatory hormone upregulation during PreD. Notably, diverging from the death of the small paradigm in Type 1 Diabetes, our data reveal a significant expansion of extra-islet endocrine clusters (EECs) that initiates during the compensatory stage, effectively preceding the onset of overt hyperglycemia. Finally, t-SNE clustering reconstructed a continuous trajectory of islet remodeling, capturing the phenotypic evolution of islets from normoglycemia through compensation to clinical decompensation. This study provides a high-resolution atlas of islet pathophysiology, offering new insights into T2D progression. HighlightsO_LIIslet remodeling during T2D progression is critically dependent on islet size. C_LIO_LIMedium and large islets density negatively correlates with HbA1c. C_LIO_LISmall islets exhibit resilience to metabolic stress during T2D progression. C_LIO_LIEECs expansion suggests a process of -cell-biased neogenesis. C_LIO_LIt-SNE maps the islet trajectory from compensation to decompensation. C_LI

pathology↗

bioRxiv2026

Wetness modulates the effects of grazing on net ecosystem productivity in global grasslands

Overgrazing has induced widespread grassland degradation globally. However, how grazing intensity affects ecosystem carbon dioxide (CO2) fluxes with wetness fluctuations in grasslands at a global scale remains poorly understood. Here we measured ecosystem CO2 fluxes covering the 7th to 11th years of a continuous grazing experiment in a typical steppe, and conducted a meta-analysis of 585 observations by collecting relevant data in global grasslands. Our experimental results showed that mean gross primary productivity (GPP) and ecosystem respiration (ER) were decreased under heavy grazing (HG) compared with control without grazing (CK), whereas net ecosystem productivity (NEP) was not different between HG and CK in the typical steppe. The NEP was higher under light grazing in the wetter years, but it was not different between LG and CK under drier years in the typical steppe. The structural equation model showed that grazing altered NEP by increasing soil temperature and relative growth rate, while decreasing AGB. In contrast, grazing decreased GPP, ER and NEP, respectively, in global grasslands. Both our field experiment and the meta-analysis revealed that the response of NEP to light grazing, rather than heavy grazing, was lineally correlated with the wetness index. Higher wetness and aboveground biomass (AGB) increased the response of NEP to grazing in global grasslands. However, heavy grazing reduced NEP and AGB even under higher wetness indices in global grasslands, resulting from a loss of their resilience in long-term heavy grazing. These findings indicate that light grazing appears to be a promising management to promote plant relative growth rate and carbon sequestration. Overall, the meta-analysis and field experiment jointly provide global perspectives on the response of ecosystem CO2 fluxes to grazing intensity and improve our understanding of the factors influencing the response of ecosystem CO2 fluxes to grazing intensity.

ecology↗

bioRxiv2026

Vitamin B12 Improves Skeletal Muscle Mitochondrial Biology in Aged Mice

Age-related skeletal muscle deterioration is a commonly reported disability among older adults, attributed to several factors including mitochondrial dysfunction, a major hallmark of aging. Therapies to attenuate or reverse mitochondrial decline are limited. Despite identified positive relationships between vitamin B12 (B12) and mitochondrial biology, the impact of B12 supplementation on skeletal muscle mitochondria, in advanced aged, has not been examined. Thus, the impact of B12 supplementation on skeletal muscle mitochondrial biology was examined in (i) aged female mice, given 12 weeks of B12 supplementation (SUPP) or vehicle control, and (ii) in human primary myotubes. In the mouse model, mitochondrial DNA and content were measured with PCR and citrate synthase activity, respectively; mitochondrial morphology was examined using transmission electron microscopy; mitochondrial function was examined using extracellular metabolic flux analysis; and proteins and pathway enrichment was identified with proteomics. In the cell model, ROS and glutathione was measured using luminescent assays. The results demonstrated that SUPP in aged mice increased muscle mitochondrial content and improved morphology. Further, differentially expressed proteins were enriched in TCA cycle, OXPHOS, and oxidative stress pathways. In the cell model, B12 supplementation reduced ROS levels. This is the first study, to our knowledge, examining the impact of B12 supplementation on skeletal muscle mitochondrial biology in aged female mice. Results suggest that B12 supplementation improves mitochondrial biology in aged female mice.

molecular biology↗

bioRxiv2026

A unified framework enables accessible deployment and comprehensive benchmarking of single-cell foundation models

Single-cell foundation models (scFMs) have been widely promoted as a unifying paradigm for transcriptomic analysis, yet whether large-scale pretraining translates into reproducible biological advantages remains unclear. Their adoption is further hindered by heterogeneous implementations, preprocessing requirements, and computational environments. Here we develop a unified, automated, and reproducible framework for standardized deployment and controlled evaluation of scFMs across datasets, computational environments, training regimes, and downstream analyses, substantially lowering the technical barriers to their use. Leveraging this framework, we systematically investigate thirteen scFMs alongside established methods across nearly one hundred datasets spanning diverse biological contexts. Our analyses reveal clear practical boundaries to scFM utility. First, increased model scale, architectural complexity, pretraining corpus size, or input encoding does not consistently translate into superior downstream performance. Instead, measurable properties of embedding geometry provide a model-agnostic, representation-level explanation for differences in zero-shot performance across diverse model families. Second, the benefits of pretrained representations depend strongly on the biological and supervision regime: scFMs provide their clearest advantages under extremely limited supervision, particularly for rare-cell annotation and open-set detection of source-absent cell states, whereas established methods remain competitive or preferable in most other settings. Task-matched analyses further show that scFM representations transfer inconsistently to spatial-domain recovery, while their gene embeddings capture broad functional relatedness without reliably recovering context-specific regulatory relationships. Together, these results establish that scFM utility is neither universal nor determined simply by model scale alone, but varies with learned representation geometry, biological context, and supervision. By combining reproducible deployment with large-scale empirical and mechanistic investigation, our framework provides a principled foundation for determining when foundation-model pretraining offers genuine practical value and when simpler approaches remain sufficient.

bioinformatics↗

bioRxiv2026

Codon Deoptimization of Multispecific Biologics Reduces Mispairing During Transient Mammalian Protein Expression

Codon optimization is utilized in biologics design to maximize protein expression. Selecting the host organisms most frequently used codons for each amino acid can significantly enhance recombinant protein expression yields. However, non-optimal codons in mRNA can be critical for functional protein production through inducing pauses in or attenuating protein translation. In our study, we have investigated the effect of deoptimizing serine codons in biologics by shifting them from the five most frequently used codons to the least (TCG). Rare serine codons were strategically inserted into the coding sequences of the constant regions in a trispecific antibody (Protein 1), a bispecific antibody (Protein 2), and multiple non-proprietary bispecific antibodies. We observed that inserting 1-2 rare serine codons within an open reading frame led to expression changes that reduced the formation of mispaired 2x light chain and half-molecule species. Protein purity was drastically increased by incorporating two deoptimized serine codons into a single chain. Notably, we observed a negative correlation between total protein expression yield and final product purity. Taken together, our work demonstrates that incorporation of deoptimized serine codons into a single chain can significantly influence multispecific biologic pairing and enhance final product purity. Our findings align with existing literature showing that rare codon usage modulates translation kinetics and protein folding. Future investigation is warranted to enable a priori identification of the rate-limiting chain in multispecific biologics, thereby guiding strategic codon deoptimization prior to expression.

bioengineering↗

bioRxiv2026

Empagliflozin alleviates doxorubicin-induced cardiotoxicity by suppressing oxidative stress via modulation of the JNK/Nrf2 signaling pathway

Doxorubicin (DOX) treatment increases the risk of myocardial dysfunction and heart failure, in which oxidative stress plays a central role. Empagliflozin (EMPA) has been shown to benefit heart failure patients, yet its underlying mechanism remains unclear. In this study, we showed that EMPA treatment improved cardiac function, ameliorated structural remodeling, and increased survival in DOX-treated mice. Furthermore, EMPA reduced DOX-induced reactive oxygen species (ROS) overproduction and myocardial injury. Through functional analysis overlapping DIC- and EMPA-regulated genes, we identified the involvement of JNK signaling in addition to redox pathways. Subsequent investigations demonstrated that EMPA restored redox homeostasis by inhibiting JNK activation, reactivating NRF2 and its downstream antioxidant proteins HO-1, NQO1, GPX4, and SOD2 both in vivo and in vitro. These protective effects were abolished by the Nrf2 inhibitor ML385 or the JNK activator anisomycin. Collectively, our findings indicate that EMPA protects against DOX-induced cardiotoxicity by modulating the JNK/Nrf2 signaling and attenuating oxidative stress. This study provides a rationale for further investigation of EMPA as a potential therapeutic strategy for chemotherapy-associated cardiac injury. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/697595v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@16743d4org.highwire.dtl.DTLVardef@96495borg.highwire.dtl.DTLVardef@aa343dorg.highwire.dtl.DTLVardef@4ba18c_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Glucose is a ligand-like trigger for secretion of postprandial GLP-1

Glucagon-like peptide 1 (GLP-1) is secreted from the intestinal L cells in a glucose-dependent manner. However, the mechanism underlying how glucose stimulates the secretion remains unclear. Here, we found that glucose at postprandial concentrations near the Km of GK for glucose ([~]10 mM), as well as nonmetabolizable glucose analogs, triggers GLP-1 secretion by intestinal L cells through directly binding to glucokinase (GK), without increasing intracellular ATP levels. We also show that in postprandially high glucose, glucose-bound GK interacts and inhibits KATP, as assessed by immunoprecipitation and FRET-FLIM analyses, as well as patch clamping. In addition, we have utilized GK mutants identified in diabetics, demonstrating that those mutants defective in binding to glucose impair GLP-1 secretion in however high glucose, whereas mutants constitutively bound to glucose with defects in catalysis, promote GLP-1 secretion even in low glucose. Furthermore, the KATP mutant unable to bind to GK blocks GLP-1 secretion in high glucose. We have also provided evidence showing that sodium-glucose cotransporter 1 (SGLT1) plays an important role in the basal secretion of GLP-1, but not in high glucose. We have thus revealed that glucose the molecule itself and GK act as a ligand and the receptor, respectively, to induce GLP-1 secretion in response to high glucose, providing new therapeutic avenues targeting metabolic diseases.

biochemistry↗

bioRxiv2025

Distinct Myogenic Stages Recapitulate Transcriptomic Networks in COPD Cachexia

BackgroundCachexia is an extrapulmonary manifestation of chronic obstructive pulmonary disease (COPD) characterized by weight loss and muscle wasting. Transcriptomic analysis of skeletal muscle may provide insight to COPD-cachexia-relevant dysregulation, including at the mitochondrial level, where dysfunction is a hallmark of muscle wasting. As muscle biopsies are invasive and yield finite tissue, human muscle derived cultures (HMDCs) can expand limited biopsy material for studying skeletal muscle dysregulation. However, utility of such models depends on their recapitulation of bulk skeletal muscle transcriptomic signatures. To address this, we tested whether COPD and COPD-cachexia dysregulated transcriptional signatures in bulk skeletal muscle are preserved across stages of early differentiation. MethodsVastus lateralis biopsies were collected from 15 (7M/8F, 64{+/-}9 years) participants; COPD n=6, COPD cachexia n=4, and n=5 age-matched controls. Cachexia was defined as weight loss coupled with reduced muscle strength, fatigue, anorexia, low muscle mass and/or systemic inflammation. Satellite cells were isolated and differentiated into HDMCs (myoblasts, myocytes, and myotubes). Transcriptomics data was generated from bulk skeletal muscle and HDMCs. Differential expression analysis identified transcripts significantly dysregulated (p<0.05) in COPD and/or COPD-cachexia. Weighted gene co-expression network analysis (WGCNA) preformed at the whole transcriptome and mitochondrial transcriptome levels, identified modules of co-expressed genes. Modules were tested for correlation with clinical traits and preservation between bulk tissue and HDMCs (Z-summary >2). Gene set enrichment analysis was performed for all modules. Results660 genes were significantly differentially expressed between COPD and control bulk skeletal muscle. The top upregulated and downregulated genes were IL21R-AS1 (Log2-Fold-Change [L2FC]=5.3, p=4.2x10-5) and top downregulated POU5F1B (L2FC=-5.8, p=3.1x10-2), respectively. Among the 492 genes significantly differentially expressed between COPD and COPD-cachexia bulk skeletal muscle. The top upregulated and downregulated genes were LINC02274 (L2FC=5.6, p=3.6x10-5) and ZFY (L2FC=-6.1, p=9.7x10-3) respectively. Modules 1, 9, A, B, D and H correlated with cachexia-relevant traits, and Modules 3, 7, G, and I correlated most strongly with COPD severity. Most modules (1, 2, 4, 7, 8, 9, A, B, H) were preserved across all states; Modules D and G were preserved in myoblasts only, and Module I in myotubes only. Preserved modules were enriched for contractile, inflammatory, oxidative phosphorylation, and fatty acid metabolism pathways. ConclusionsCo-expression modules linked to COPD and COPD-cachexia in bulk skeletal muscle were broadly preserved across all differentiation stages, with myoblast and myotubes most completely recapitulating disease-relevant transcriptional signatures. These findings support HMDCs, as tractable in vitro models preserving contractile, inflammatory, and mitochondrial signatures of COPD-associated muscle dysfunction.

genetics↗

bioRxiv2025

Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Mendels law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin-antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster, optimized YYAP strain K711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

molecular biology↗

bioRxiv2025

Structural and functional insights into QueC-family protein in QatABCD anti-phage system

QatABCD is a widespread prokaryotic anti-phage defense system comprising four protein components, out of which QatC, a QueC-family protein is the signature component. QueC family proteins are nucleoside biosynthesis enzymes involved in the biosynthesis of queuosine, a 7-deazaguanine derivative. Recently, QueC-family proteins were shown to catalyze a deazaguanylation protein-nucleobase conjugation reaction in type IV CBASS antiphage defense. However, the mechanism of QatABCD, even the function of QatC in this system, remains unknown. Here, we demonstrate that QatBCD forms a complex in which QatD is highly flexible. Crystal structures of the QatBC complex in apo and ATP-bound form support a shared role for QueC-family proteins in targeting protein substrates for N-terminal modification as in type IV CBASS. We show that the QatB N-terminal loop, its binding with QatC and QatC catalytic site are essential for QatABCD defense in vivo, suggesting a modification might occur analogous to CBASS. These findings provide structural and functional insights into QueC-family protein in QatABCD system, suggesting the conserved mechanisms and critical roles of QueC-family in prokaryotic immunity.

biochemistry↗

bioRxiv2025

Cohesin Acetylation and ATPase Activity Control Cohesion and Loop Architecture through Distinct Mechanisms

Cohesin is a conserved protein complex that mediates sister chromatid cohesion, chromosome condensation, gene regulation, and DNA repair. These processes rely on cohesins ability to tether sister chromatids and form chromatin loops, which depend on cohesins ATPase activity and Eco1-mediated acetylation of two lysine residues (K112 and K113 in budding yeast) in its Smc3 subunit. How cohesins ATPase activity and acetylation integrate to control cohesin functions remains poorly understood. Here, we analyzed chromatin architecture in yeast mutants with altered cohesin acetylation and/or ATPase activity. We find that acetylation of either K112 or K113 is sufficient to produce a wild-type chromosome structure with loops positioned at cohesin-associated regions (CARs), whereas loss of acetylation at both residues abolishes positioned loops, indicating that acetylation at either lysine alone can maintain wild-type chromatin architecture. We further show that a cohesin acetylation mutant, despite being defective in sister-chromatid tethering and thus failing to establish cohesion, still forms wild-type-like loops, while cohesion-competent mutants lack positioned loops. These results suggest that the activities required for cohesion and loop formation are mechanistically separable, arguing against passive loop capture. Moreover, a mutant with reduced ATPase activity showed a loop profile similar to wild type, indicating that cohesin with lower ATPase activity can still form wild-type chromatin architecture. By contrast, hyper-ATPase mutants accumulate positioned loops, suggesting that increasing ATPase activity can enhance loop processivity. Together, our findings support a multilayered regulatory model in which acetylation fine-tunes ATPase output and cohesin functions to shape genome architecture.

genetics↗