Biology subjects

Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s

The model plant Arabidopsis thaliana has been a workhorse of plant biology since the 1950s, when the Columbia-0 (Col-0) accession was widely adopted by the research community as a reference genotype. Since then, Col-0 seeds have been shared among laboratories worldwide and propagated independently, creating a network of related laboratory lineages. Here, we sequenced the genomes and DNA methylomes of 78 Col-0 strains from laboratories and stock centers around the world to assess the genetic and epigenetic variation accumulated during this period and to reconstruct their propagation history from de novo variants. After quality filtering, we identified 1,415 single-nucleotide polymorphisms and 169,677 epimutations across 75 Col-0 lines and used these variants to generate SNP- and epimutation-based phylogenies. The two phylogenies showed highly concordant topologies, but the epimutation-based tree provided greater resolution of relationships among closely related lineages. Divergence-time estimates suggest that many lines have been propagated for approximately one generation per year over several decades, resulting in pairwise divergences of up to approximately 100 generations. We further identified 170 nonsynonymous substitutions and more than 200 candidate epialleles, some of which were associated with gene-expression differences among Col-0 clades and may therefore have functional consequences. Together, these findings show that Col-0 is best viewed not as a single invariant reference genotype, but as a collection of related laboratory lineages that have accumulated genetic, epigenetic, and transcriptional divergence through time, with potential consequences for the reproducibility of experiments across laboratories. Significance StatementThe Arabidopsis Col-0 reference accession is often treated as a single, invariant genotype, yet independently maintained laboratory stocks have accumulated substantial genetic, epigenetic, and transcriptional divergence since the 1950s. Some lineages are separated by more than 100 generations of independent propagation. Mutations and CG epimutations reconstruct nearly identical lineage histories, demonstrating that heritable DNA methylation changes provide a robust record of recent laboratory evolution.

genetics↗

bioRxiv2026

Locating Evolutionary Rate Inflection Points on Whole-Genome SNV Similarity Curves and Their Application in Identifying Key Mutations in Language/Cognition Genes

Language genes can be tentatively considered as a subset of cognitive genes, although they are often discussed separately. During the evolution of SNVs (single nucleotide variations) in cognition-related genes, do language genes and cognitive genes exhibit significantly different intensities of change at several key evolutionary moments--namely, the inflection points or derivative peak positions of similarity curves drawn from multi-SNV locus bases across samples? In this study, nine distance/similarity metrics (Bray-Curtis, Cosine, Pearson, Spearman, Hamming, Jaccard, Matching, Kulczynski, and Gower) were employed to analyze 413 samples from 11 taxonomic groups, targeting SNV loci in language/cognition-related genes (13,415 effective loci, approximately 400 loci per gene), with pp6 (Homo_sapiens.GRCh38) as the reference. For each method, sample similarities (defined as 1/(1+distance)) were independently sorted in ascending order to generate raw similarity scatterplots. Due to the large sample size and representativeness, the scatter density on the similarity curves was high, and no smoothing was applied. Derivative values were calculated from adjacent similarity differences to identify peaks of evolutionary rate change (top 10 peaks per method). Combined with functional annotations of 33 language/cognition-related genes, we quantified the difference scores and occurrence frequencies of the two gene categories at the peak positions. The results indicate that cognitive-related genes exhibit slightly higher occurrence frequencies in peak windows and higher average difference scores per gene than language genes. Comparative analysis of SNVs at the peak samples and their left-side windows revealed that at positions 381-382, all nine methods shared three intersecting mutation loci, involving language genes (NFXL1, SRGAP2, SRGAP2C); at positions 355-356, there was one intersecting mutation locus, involving a language gene (SRGAP2). This suggests that certain mutations in language genes may have played a distinctive role at critical junctures in the evolution of cognitive abilities.

molecular biology↗

bioRxiv2026

Epitope-Focused Immunogens Confer Broad Protection against Coronaviruses

Variable regions in coronavirus spike dominate antibody responses elicited by infection or conventional vaccination and limit induction of broad neutralization. In contrast, conserved S2 elements, including the stem helix (SH) and fusion peptide proximal region (FPPR), are promising but subdominant targets of protective immunity. Here, we employed computational design to generate de novo epitope-focused immunogens that precisely present the SH and FPPR epitopes. Formulated as combinatorial immunogens, this vaccine elicited consistent serum responses with broad reactivity across known human coronaviruses and induced epitope-specific antibodies with broad neutralizing activity. As a heterologous boost, epitope-focused immunogens protected mice against challenge with phylogenetically distinct coronaviruses, including bat SARS-related RsSHC014-CoV and MERS-CoV, establishing a generalizable strategy for precision immune focusing and advancing universal coronavirus vaccine development.

bioengineering↗

bioRxiv2026

Beyond Respiration: Heme A Synthase (CtaA) Orchestrates Hydrogen Sulfide Production and Virulence via Metabolic Reprogramming in Staphylococcus aureus

Endogenous hydrogen sulfide (H2S) serves as a pivotal gasotransmitter conferring antimicrobial resistance and shielding bacteria from oxidative stress. While cystathionine {gamma}-lyase (CSE)-dependent H2S production is critical for Staphylococcus aureus survival, the upstream regulatory nodes linking metabolic status to H2S-mediated redox defense remain elusive. Here, we identify heme A synthase (CtaA) as a master regulator that couples respiratory metabolism with H2S biosynthesis, specifically under glucose-depleted conditions mimicking host niches such as abscesses and phagosomes. Using a Himar1 transposon screen followed by a high efficiency detection method, we demonstrate that CtaA deficiency precipitates a catastrophic collapse in H2S levels (<10% of wild-type), leading to severe virulence and antimicrobial resistance changes. Specifically, the {Delta}ctaA mutant exhibits attenuated hemolytic activity and significantly reduced virulence in a Galleria mellonella model, despite displaying paradoxical resistance to specific antimicrobials. Mechanistically, CtaA deletion triggers a maladaptive metabolic reprogramming characterized by the downregulation of the L-cysteine transporter TcyP and dysregulation of arginine metabolism, which collectively impair the bacteriums capacity to produce endogenous H2S to defense oxidative stress. Notably, this redox vulnerability is linked to altered endogenous nitric oxide (NO) dynamics, suggesting a disrupted H2S-NO crosstalk essential for stress adaptation. Our findings elucidate a novel metabolic-redox axis where CtaA governs H2S homeostasis to counteract host-imposed oxidative stress. Targeting the CtaA-H2S axis represents a promising therapeutic strategy to sensitize S. aureus to host immune clearance by dismantling its critical redox shield.

microbiology↗

bioRxiv2026

Probing Mechanisms of Allosteric Regulation in AAA+ ATPases for Microtubule Severing and Protein Disaggregation

Ring-like AAA+ (ATPases Associated with diverse cellular Activities) biological machines mediate protein remodeling to assist a broad range of essential cellular functions. The nucleotide-dependent remodeling action involves intra- and inter-ring allosteric communication to generate mechanical force applied onto the substrate by a set of loops that protrude into the central channel. In this study, we probe these allosteric mechanisms through a comparative study of the katanin, a microtubule severing protein including a clade 3 AAA domain, and the double-ring ClpB, a protein disaggregase including both a clade 3 and a clade 5 AAA domain. Our molecular dynamics simulations, combined with machine learning and bioinformatic analysis, reveal both similar mechanisms involving the clade 3 domain and ClpB-specific ones involving communication with the clade 5 domain. We find that both nucleotide and substrate polypeptide binding restrict the conformational landscape sampled by katanin and ClpB, with ligand-specific conformations observed in the latter case. Allosteric contributions of secondary structure elements, ranked by using SHapley Additive exPlanations analysis in machine learning approaches and binary classification of features in ligand states, highlight the important role of regions adjacent to the nucleotide-binding site and the pore loops. Amino acid-level analysis of the allosteric paths reveals that intra-ring cooperativity modulates long-distance communication within the AAA+ protomers.

biophysics↗

bioRxiv2026

Spatiotemporal coordination of specialized cerebellar networks supports episodic memory in older adults

Episodic memory decline in ageing is typically attributed to the cortico-hippocampal system, yet the cerebellums specific contribution via cerebellar-cerebral circuits remains underexplored. We analysed task-based fMRI data from 821 older adults, including a longitudinal subset of 78 participants followed for four years. Using sparse dictionary learning on task-responsive activity, we identified three non-motor networks: a bilateral lobule VI/Crus I mnemonic-monitoring network, a right lobule Crus I/II default-mode-aligned network, and a right lobule VIIb/VIIIa evidence-evaluation network. While network recruitment varied with task demands and associated with memory performance, phase-specific static cerebellar-cerebral functional connectivity showed stable organization but limited behavioural specificity. In contrast, dynamic functional connectivity patterns effectively distinguished memory-performance groups. Crucially, greater instability in dynamic functional connectivity during encoding predicted longitudinal retrieval slowing. These findings suggest that preserved episodic memory in older adults is supported by the spatiotemporal coordination of specialized cerebellar networks with distributed cerebral networks.

neuroscience↗

bioRxiv2026

Reconstructing lineage-constrained gene-program dynamics with PhyloFM

Cell-fate dynamics are defined not only by where cells end, but by when fate programs emerge, diverge, and reshape population structure. Much recent effort has been devoted to reconstructing these dynamics from temporally resolved single-cell RNA-seq and spatial transcriptomics. However, it is difficult because these measurements only provide destructive snapshots instead of continuous molecular histories. On the other hand, a diverse set of lineage-tracing methods are now available which could serve as temporal constraints to connect the dots. The challenge is how to utilize and unify these diverse ancestry records in the reconstruction of a continuous cell state dynamics. Here we introduce PhyloFM, a lineage-constrained flow-matching framework that maps heterogeneous lineage information onto a cell-fate-anchor topology and learns a continuous velocity field together with relative cell-abundance changes on a topology-regularized latent geometry. From the same integrated trajectories, PhyloFM predicts population transport, future fate probabilities, commitment timing and branch-resolved projected gene- and module-level dynamics. We tested PhyloFM across five lineage-tracing settings spanning C. elegans embryogenesis, LARRY hematopoiesis, pandaCREST ventral-midbrain development, zebrafish heart regeneration and spatial eTracer tumours. In C. elegans, our method improved population transport by 17.3% and lineage-grounded dynamic error by 16.3% relative to state-of-the-art dynamical baselines, with transport error reduced by 26.6% relative to additional lineage-aware control. Independent EPIC GFP reporter traces support the inferred timing of proneural, ciliated-neuron and late-selector programs, with 67% of matched reporter genes showing Pearson r > 0.6. On the spatial eTracer tumour benchmark, PhyloFM increased clone-grounded fate accuracy by 70.4% relative to the best spatial baseline. Together, these analyses show that diverse lineage records can serve as biological constraints for reconstructing continuous, interpretable molecular fate dynamics from single-cell snapshots.

bioinformatics↗

bioRxiv2026

Sleep reactivation of positive self-evaluation reveals neural-evaluative alignment that varies with depressive symptoms

Positive self-evaluation underpins resilience and mental health, yet how to enhance positive self-evaluation and the underlying neurocognitive mechanisms remain poorly understood. Existing data mostly examined self-evaluative processing of the wakeful minds, with the role of sleep remain unexplored. Here, we demonstrated that reactivation of positive self-evaluation during sleep revealed fine-grained neural-evaluative alignment that varies with depressive symptoms. We found that targeted reactivation of positive personality traits during non-rapid eye movement (NREM) sleep enhanced positive self-evaluation, but this benefit diminished with elevated depressive symptoms. Moreover, cueing positive traits during NREM sleep elicited trait-specific, 11-16 Hz EEG sigma power-based neural representations that aligned with post-sleep positive self-evaluative representational structures, as revealed by representational similarity analyses. Notably, individuals with elevated depressive symptoms exhibited weaker neural-evaluative representational alignments, identifying a maladaptive self-evaluative processing that bridges across sleep and wakefulness states. These findings provide mechanistic insights on how fine-grained neural-evaluative alignment can substantiate positive self-evaluation, and why it was disrupted as depressive symptoms increased. HighlightsO_LIPositive-trait reactivation during NREM sleep enhances positive self-evaluation C_LIO_LIThis behavioral benefit decreases as depressive symptoms increase C_LIO_LISleep cueing evokes trait-specific sigma-band neural representations C_LIO_LINeural-evaluative alignment weakens as depressive symptoms increase C_LI

neuroscience↗

bioRxiv2026

Diatoms maintain metabolic activity in deep ocean twilight zones

Phytoplankton are primarily confined to the sunlit epipelagic zone, yet intact algal cells persist in the oceans mesopelagic twilight zone where light is minimal. However, their survival strategies in the deeper ocean remain unknown. Here, we isolate Chaetoceros sp. DS1 from 1000 m depth and reveal its survival mechanisms under prolonged darkness and high pressure, including membrane lipid remodeling and enhanced antioxidant defenses. Importantly, DS1 maintains a latent photosynthetic reserve that activates upon exposure to dim blue light and higher pressure typical of the twilight zone, enabling photosynthesis and nutrient uptake. It exhibits metabolic flexibility by utilizing stored carbon in darkness and assimilating organic carbon under dim light. Global meta-omics data show widespread, transcriptionally active Chaetoceros-like diatoms in the twilight zone, expressing blue-light sensors and protein synthesis genes. These findings identify the ocean twilight zone as a previously overlooked niche for metabolically active phytoplankton, expanding understanding of deep-ocean microbial ecology and carbon cycling.

ecology↗

bioRxiv2026

Retinal electrical synapse plasticity is required for optimal visual performance

Most electrical synapses in the mammalian central nervous system are composed of Connexin 36 (Cx36). Electrical synapses are functionally plastic, changing their degree of coupling based on the activity of the cell or connected cells, or based on activation of neurotransmitter or neurohormone receptors. Plasticity can reach an extreme in which electrical synapses become functionally silent, which is a normal operational condition for some circuits. Cx36 coupling is regulated by phosphorylation, which opens the channels. In retinal circuits, Cx36 is often maintained in a poorly phosphorylated, poorly coupled state. We reasoned that phosphomimetic mutants of Cx36 could remain constitutively open and maintain circuits in a well-coupled state that will interrogate the need for plasticity. We developed a constitutively open Cx36 mutant by systematically replacing phosphorylatable residues that regulate coupling with acidic residues. Single mutants of serine 315 significantly modified functional regulation of coupling in HeLa cells, but mutation of four residues was required to produce a mutant that was constitutively open. This mutant, Cx36-S110D, T111E, S293D, S315D, called Cx36-DEDD, displayed high coupling in control conditions and only modest changes under phosphorylating and dephosphorylating conditions. We developed a conditional knockin mouse that expresses Cx36-DEDD and cytoplasmic tdTomato in cells that expressed Cre recombinase. When crossed with Six3-Cre mice, Cx36-DEDD expressed widely in the retina including in photoreceptors, bipolar, amacrine and ganglion cells. Rod-cone electrical coupling displayed the maximum of its physiological dynamic range, and photopic visual acuity and contrast sensitivity were significantly reduced in Cx36-DEDD homozygous animals. We conclude that reduction of coupling in some retinal circuits is required for optimal daylight vision. Significance StatementTwo types of synapses, chemical and electrical, work together throughout the central nervous system to perform neurological functions. While it is widely understood for chemical synapses that plasticity, changing the strength of synaptic connections, plays critical roles in many processes, this is far less understood for electrical synapses. By developing an electrical synapse protein mutant that locks channels in an open state, we have investigated retinal circuits that retain functional electrical synapses but lack their latitude for plasticity. This perturbation significantly compromises visual acuity and contrast sensitivity in the daylight, revealing that electrical synapse plasticity is necessary to tune retinal functions for optimal performance. Thus, electrical synapse plasticity along with chemical synapse plasticity is required for neural function.

neuroscience↗

bioRxiv2026

ERK signaling integrates multiple mechanisms to drive cortical evolutionary expansion

A critical first step in human evolutionary divergence from chimpanzees and other primates is the production of greatly increased numbers of cortical pyramidal neurons during development and over evolutionary time. This expansion underpins the enlarged human cerebral cortex and, consequently, higher-order cognition and consciousness. However, the cellular and molecular mechanisms driving this progressive increase in cortical neuron number remain incompletely understood. Here we show that elevated ERK signaling in human cortical radial glia (RGs), relative to mouse RGs, arises from evolutionary changes in the developmental expression of existing shared genes. Using the Emx1-Cre line to overexpress MEK1DD, a constitutively active mutant of rat MAP2K1, we found that enhanced ERK signaling in mouse cortical RGs upregulates cAMP-PKA signaling, along with promoting self-renewal, expanding the RG pool, and accelerating cell cycle progression. Conversely, overexpression of PKA signaling in mouse cortical RGs via in utero electroporation of constitutively active PRKACA mutants (L206R or W196G) reduces ERK activity, prolongs the cell cycle, suppresses SHH-SMO and YAP/TAZ pathway activity, and blocks ependymal gliogenesis. Together, our results demonstrate that ERK and PKA signaling in cortical RGs engage a dynamic balance of synergistic and antagonistic interactions. This interplay couples evolutionarily enhanced ERK and PKA activities to increased cortical RG numbers, prolonged cell cycle progression, and an extended neurogenic period, which collectively culminate in a marked increase in neuronal production. We conclude that heightened ERK pathway activity in cortical RGs serves as a central driver of progressive neocortical expansion across mammalian evolution. Significance StatementThe human brains extraordinary cognitive abilities stem from a dramatic increase in cortical neuron numbers during evolution. This study reveals that enhanced ERK signaling in human cortical radial glia neural stem cells, relative to other primates, is a key driver of this expansion. By manipulating this pathway in mice, we demonstrate that ERK coordinates multiple mechanisms--including self-renewal, cell cycle acceleration, and a dynamic interplay with PKA signaling--to boost neuronal output. These findings identify a core molecular axis underlying mammalian cortical evolution and provide a framework for understanding how the human cortex acquired its unique size and, consequently, its remarkable complexity.

developmental biology↗

bioRxiv2026

Nutrient flux governs osteogenic fate commitment through the SLC3A1-cystine Axis

Skeletal and mesenchymal cells have limited bone-forming potential due to their rarity, tendency for senescence and/or unstable osteogenic lineage commitment. We previously identified an osteopotent CXCR4 stem cell population with unclear mechanism for its differentiation potential. Here, we found that the cystine transporter SLC3A1 was selectively enriched in CXCR4+ stem cells, uncovering a role for amino acid transport in regulating osteogenic fate commitment. Enforced SLC3A1 expression reprogrammed mesenchymal cells toward a stable osteogenic state while suppressing adipogenic differentiation. Mechanistically, SLC3A1-mediated cystine flux established a glutathione-dependent metabolic program that preserved mitochondrial fitness and restrained stem cell senescence. SLC3A1 also stabilized IGF-1 through suppression of ZMYND8-mediated ubiquitination, uncovering ZMYND8 as a previously unrecognized E3 ligase regulating osteogenic commitment. Cystine supplementation phenocopied the effects of SLC3A1 activation, promoting osteogenic differentiation and skeletal regeneration without genetic manipulation. In vivo, cystine administration accelerated bone regeneration and attenuated ovariectomy-induced bone loss, while analyses of a human osteoporosis cohort, osteoporotic specimens, and single-cell transcriptomic datasets revealed coordinated suppression of the SLC3A1-cystine-IGF-1 pathway in osteoporotic mesenchymal cells. Taken together, these findings establish SLC3A1-mediated cystine transport as a programmable metabolic determinant of osteogenic fate commitment and identify cystine metabolism as a therapeutically targetable axis for skeletal regeneration and osteoporosis.

cell biology↗

bioRxiv2026

GatorPrism: Prototype-Conditioned Routing across Coalition Graph Experts for Spatial Multi-Omics Integration

Spatial multi-omics integration requires balancing cross-omics consensus with modality-specific signals whose importance varies across tissue locations. We present GatorPrism, a self-supervised coalition graph mixture-of-experts framework that explicitly separates cross-omics consensus from modality-specific structure and adaptively integrates their contributions across tissue locations. A joint expert encodes an intersection-based consensus graph, while modality-private experts capture mixed spatial-molecular structures; a prototype-conditioned router assigns spot-specific coalition weights. GatorPrism is trained end-to-end to preserve shared and modality-specific neighborhoods, align co-registered modalities, maintain spatial coherence, and prevent routing collapse. Across eight spatial multi-omics datasets, GatorPrism achieved strong performance across nine clustering metrics against nine competing methods. In human tonsil, inferred domains were supported by concordant RNA and ADT markers and distinct functional programs. In embryonic mouse brain, routing profiles revealed anatomically localized shared, RNA-private, and ATAC-private states supported by transcriptomic, chromatin-accessibility, and motif evidence. These results establish GatorPrism as an accurate and interpretable framework that reveals how shared and modality-specific molecular signals organize tissue structure. Source code is available at https://github.com/Gator-Group/GatorPrism.

bioinformatics↗

bioRxiv2026

Machine Learning-Assisted Evolution of Broadly Functional Enzyme Libraries

Biocatalysis offers sustainable solutions to pressing challenges in chemical synthesis by exploiting the remarkable efficiency and selectivity of enzymes. Importantly, enzymes are able to accommodate non-native substrates and mediate transformations outside of their natural repertoire. Enzymes can be engineered for diverse applications by harnessing these promiscuous activities and optimizing them using directed evolution (DE). The success of a DE campaign, however, depends on the availability of a protein starting point that displays detectable levels of the desired function. To find a starting point, researchers often screen libraries of protein variants for novel activities, typically with low rates of success. Here, instead, we diversified the active site of a desirable parent protein and applied machine learning to generate informed, promiscuous libraries of protein variants. Specifically, we tested 26 different carbene and nitrene transfer reactions and used active learning-assisted directed evolution (ALDE) to generate optimized protoglobin variants with high activity across multiple reactions. We observed improvements in activity and selectivity for every reaction performed by the parent enzyme in at least one member of the ALDE-predicted libraries. Moreover, variants from these libraries can catalyze 5 out of 10 reactions not catalyzed by the parent protoglobin. These results indicate that supervised machine learning can help guide the construction of high-value enzyme libraries with expanded catalytic scope. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/740427v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@fc2071org.highwire.dtl.DTLVardef@b5e787org.highwire.dtl.DTLVardef@737976org.highwire.dtl.DTLVardef@12b5e51_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Pervasive historical introgression across oak phylogeny shapes gene expression

Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.

evolutionary biology↗

bioRxiv2026

ITPKB is a conserved regulator of natural killer cell desensitization/education that constrains antitumor immunity

Natural Killer (NK) cell desensitization induced by persistent stimulation limits durable antitumor immunity, yet the molecular mechanisms governing this dysfunctional state remain poorly defined. To identify conserved regulators of NK cell desensitization, we performed comparative transcriptomic analyses across multiple murine models of persistent activation and dysfunction. This approach defined a shared transcriptional program of desensitization and identified Itpkb to be upregulated across multiple distinct contexts. Genetic and pharmacological inhibition of ITPKB enhanced degranulation, cytokine production, and cytotoxicity in both murine and human NK cells under multiple desensitization settings. Mechanistically, ITPKB regulated signaling downstream of persistent activation through the IP3/IP4 axis, limiting calcium mobilization and NFAT-dependent transcriptional responses in desensitized NK cells. Furthermore, inhibition or deletion of ITPKB enhanced NK-cell mediated tumor control in vivo and improved the efficacy of adoptively transferred CAR-NK cells, underscoring the translational potential of targeting this pathway. Together, these findings identify ITPKB as a cell-intrinsic regulator of NK cell desensitization and support targeting the IP3/IP4 signaling axis to enhance NK cell-mediated antitumor immunity.

immunology↗

bioRxiv2026

VDAC2 stabilizes a membrane-inserted, primed intermediate of BAX activation

BAX, a major effector of mitochondrial apoptosis, is activated through a series of conformational transitions that lead to mitochondrial outer membrane permeabilization. Genetic studies have established VDAC2 as an essential regulator of BAX-mediated apoptosis, yet the molecular basis of this regulation remains unresolved. The absence of direct structural and biochemical characterization of VDAC2-BAX interactions has prevented mechanistic understanding of how VDAC2 influences BAX activation. Here, using complementary biochemical, biophysical and structural approaches, we reconstituted and characterized a stable VDAC2-BAX complex that was not observed with VDAC1, highlighting an isoform-specific role in BAX regulation. We show that VDAC2 captures and stabilizes a primed BAX conformation displaying the hallmarks of activation, including membrane insertion, BH3 exposure, and increased accessibility of the N-terminal activation region. By integrating AlphaFold3 predictions with molecular dynamics simulations, biochemical, biophysical and structural constraints, we derive an experimentally-supported structural model in which BAX is anchored through its 9 helix while its soluble domain partially extends over the VDAC2 pore. Together, our findings support a model in which VDAC2 facilitates BAX membrane insertion and stabilizes a membrane-inserted, activation- competent BAX intermediate. Rather than serving as a structural component of apoptotic pores, VDAC2 acts as a regulatory checkpoint in BAX activation. These results provide a molecular explanation for the emerging role of VDAC2 in mitochondrial apoptosis and establish structural basis for a previously inaccessible intermediate in the BAX activation pathway.

biochemistry↗

bioRxiv2026

Optogenetic decoupling of ODC inhibition and degradation reveals a requirement of polyamine oscillation for cell cycle progression

The dysregulation of polyamine homeostasis is a fundamental hallmark of both cancer and aging. Ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine synthesis, is regulated by the antizyme OAZ1 through a dual mechanism: inhibition of enzymatic activity and induction of proteasomal degradation via a C-terminal degron. In Bachmann-Bupp syndrome (BABS), mutations in this degron lead to ODC accumulation and toxic polyamine levels. However, the functional coupling between ODC inhibition and degradation remains poorly understood, and the current therapeutic intervention with DFMO target enzymatic activity without addressing protein accumulation. Here, we developed an optogenetic yeast model of BABS to decouple ODC inhibition from its degradation. By fusing a light-switchable LOV2-based module to a truncated, degron-less yeast ODC, we created a system where ODC degradation is controlled by light, independent of OAZ1 binding. We demonstrate that the loss of the ODC degron mimics the BABS cellular phenotype, characterized by increased polyamines, elevated ROS, and growth arrest. Crucially, while constant light-induced degradation is insufficient to rescue growth, oscillating ODC degradation at a 40-minute period restores polyamine homeostasis, cell cycle progression, and cellular growth. Our findings demonstrate that the inhibitory and degradation-inducing roles of OAZ1 can be decoupled and highlight the necessity of periodic polyamine oscillation for the cell cycle. Our work would be of great value for understanding the regulation mechanism of the polyamine metabolic network and establishing new targeted therapeutic strategies. Significance statementMutations in ODC degron lead to ODC accumulation and toxic polyamine levels in BABS. While DFMO has provided clinical relief for BABS patients, its utility is limited because it only inhibit ODC activity. We utilized an optogenetic approach in Saccharomyces cerevisiae to bridge this knowledge gap. We successfully decoupled the inhibitory and degradation-inducing functions of the ODC-OAZ1 axis and achieved three significant biological insights. First, we established yeast as a powerful and versatile model for investigating of the molecular mechanisms of BABS. Second, we demonstrated that the inhibitory and degradation-inducing roles of OAZ1 can be decoupled under specific conditions. Third, we revealed that periodic oscillation in polyamine levels is essential for maintaining proper cell cycle progressing.

molecular biology↗