Biology subjects

Li, X.

Publications and source records attributed to Li, X..

At least 199 records · Page 11Linked to original sources

bioRxiv2026

An LSEC-focused computational drug repurposing platform for liver fibrosis: Identification of vorinostat and other LSEC-protective candidates

Liver sinusoidal endothelial cells (LSECs) are increasingly recognized as a critical yet underexplored cell type in anti-fibrotic drug development. This study presents a computational drug screening platform integrating LSEC-specific transcriptomic analysis across simple steatosis, fibrotic nonalcoholic steatohepatitis (NASH), and cirrhosis, with tiered gene signature selection combining machine learning, large language model-assisted curation, gene safety assessment, and Connectivity Map-based screening using human endothelial perturbational profiles. The platform identifies 6 clinical-stage and 8 preclinical candidates with LSEC-protective potential. Among these, vorinostat (SAHA), a clinically approved histone deacetylase (HDAC) inhibitor, is selected for experimental validation. In hepatocyte-specific Asah1-deficient mice fed a Paigen diet, SAHA attenuates hepatic inflammation, fibrosis, LSEC dysfunction, and portal hemodynamic abnormalities, with effects confirmed in a hepatotoxin (CCl4)-induced fibrosis model. High mobility group box 1 (HMGB1) is identified as a key hepatocyte-derived paracrine mediator of LSEC injury through Transwell co-culture and glycyrrhizin rescue. Vorinostat dose-dependently reverses HMGB1-induced LSEC dysfunction across inflammation, capillarization, fibrogenesis, and vasoconstriction, associated with endothelial transcription factor reprogramming including KLF2 upregulation, validated in primary LSECs and in vivo. SAHA also protected LSECs from TNF--induced inflammation and reduced monocyte adhesion. These findings establish an LSEC-focused drug repurposing framework and identify candidates for LSEC-protective anti-fibrotic therapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/727430v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@41e95dorg.highwire.dtl.DTLVardef@1401031org.highwire.dtl.DTLVardef@e72fc4org.highwire.dtl.DTLVardef@1f11347_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Cobamide-Dependent Dichloromethane Fermentation by Dehalobacter Reveals a Hidden Acetogenic Route for Organohalide Biotransformation

Halogenated one-carbon (C1) compounds, such as dichloromethane (DCM), drive critical fluxes in global carbon and halogen cycles. While the genus Dehalobacter is canonically defined by obligate organohalide respiration, its physiological and ecological roles in anaerobic C1 metabolism have remained fundamentally ambiguous. Here, we document a paradigm-shifting metabolic capacity within a sediment-derived microbial consortium: the autonomous fermentation of DCM by a novel population, Candidatus Dehalobacter formatiformans strain J1. Over successive transfers, strain J1 outcompeted co-existing Dehalobacterium formicoaceticum to become the overwhelmingly dominant population (>80% relative abundance), converting DCM stoichiometrically to acetate and formate (4:1) without auxiliary substrates. Genome-resolved metagenomics revealed that strain J1 couples a distinct mec gene cassette--mediating methyl-transfer reactions during DCM activation--to a complete Wood-Ljungdahl pathway for efficient C1 assimilation. Crucially, strain J1 lacks the complete genetic repertoire for de novo cobamide biosynthesis. Physiological validation confirmed that this fermentative pathway is strictly dependent on exogenous cobamides, exposing a profound reliance on community cross-feeding. These findings reveal an unexpected acetogenic lifestyle within Dehalobacter, a lineage historically viewed as comprising obligate organohalide-respiring bacteria. More broadly, this work identifies cobamide-dependent methyl-transfer metabolism as an ecological control on anaerobic DCM fermentation and expands the known roles of Dehalobacter in carbon-halogen cycling in anoxic environments.

microbiology↗

bioRxiv2026

A Cross-tissue Temporal Multi-omics Atlas Reveals the Molecular Architecture of Pressure Injury

Pressure injury induces progressive necrosis of skin and deep muscle, yet how mechanical loading reshapes molecular programs across tissues and time remains poorly defined. To address this gap, we established a rat pressure-injury model and performed longitudinal integrated profiling of skin and deep muscle across four stages, combining transcriptomics, proteomics and untargeted metabolomics with histological assessment. This multi-layered atlas revealed a staged injury program dominated by early transcriptional activation of innate immunity and complement-coagulation crosstalk, accompanied by neutrophil-associated responses and engagement of upstream regulatory networks. As injury advanced, a second axis of remodeling emerged, characterized by sustained suppression of mitochondrial energy metabolism and oxidative phosphorylation, particularly in muscle, together with extracellular matrix and adhesion rewiring. In parallel, skin preferentially activated barrier-repair and protein-homeostasis programs, including keratinization and autophagy-linked processes, indicating tissue-specific adaptation to the same mechanical insult. Temporal clustering and pathway-network analysis further showed that immune activation and metabolic collapse are not independent events but are dynamically coupled across stages, with muscle exhibiting broader molecular reprogramming and a stronger shift toward irreversible structural failure. Together, these data define a cross-tissue, stage-resolved molecular framework for pressure injury progression and identify pathway-level windows that may inform tissue-targeted and stage-specific intervention strategies.

systems biology↗

bioRxiv2026

Biosynthesis of bisbenzylisoquinoline alkaloids

Bisbenzylisoquinoline alkaloids (bisBIAs) are pharmacologically valuable plant metabolites with complex stereochemical architectures, yet the catalytic principles governing their assembly have remained largely unclear. Here, we elucidate the enzymatic pathway to cyclic bisBIAs and uncover a non-canonical redox-mediated mechanism for post-assembly stereochemical control. We identify cytochrome P450 enzymes that catalyze regioselective oxidative dimerization and macrocyclization of benzylisoquinoline monomers, establishing the macrocyclic scaffold. Subsequent stereochemical specification is achieved by a paired oxidase-reductase module that selectively epimerizes a single stereocenter through a transient imine formation, converting (R,S)-configured intermediates to (S,S)-products. Reconstitution of the pathway in yeast enabled production of both native bisBIAs and non-natural analogs, demonstrating pathway modularity and engineering potential. These results establish the biochemical principle underlying bisBIA biosynthesis and provide a framework for programmable biosynthesis of these complex natural products.

biochemistry↗

bioRxiv2026

SpatialClaw: A Memory-Augmented Autonomous Ecosystem for Spatial Omics Analysis

While the expansion of spatial omics has revolutionized our ability to dissect tissue architecture, the accumulation of incompatible computational methods has heavily fragmented end-to-end analysis, rendering complex workflows irreproducible. Generic conversational agents lack the domain-specific precision necessary to navigate the intricate biological pipelines. To overcome this, we present SpatialClaw, a memory-augmented autonomous ecosystem to unify spatial omics analysis under a single natural-language interaction. SpatialClaw integrates 30 specialized skills, spanning raw data preprocessing, spatial domain identification, deconvolution, spatially variable gene detection, cell-cell communication analysis, multi-sample and cross-modality integration. Distinct from existing agents, SpatialClaw introduces a graph-based persistent memory architecture that stores dataset metadata, analysis lineage, biological insights, and user preferences as versioned nodes and edges across three hierarchical layers (Session, Episodic, and Semantic), governed by a deterministic promotion policy. A Memory-Augmented Reasoning (MAR) Operator bridges the memory store and the main agent, synthesizing retrieved experiences into task-specific guidance for each query. In rigorous benchmarking spanning three memory-sensitive scenarios across 10 spatialomics skills, SpatialClaw outperforms both a standard large language model and the memory-only configuration. Furthermore, we demonstrate its robust biological utility by dissecting the complex tumor microenvironment of a 15-section human triple-negative breast cancer cohort. In merely three conversational turns and with zero direct scripting, SpatialClaw executes a comprehensive end-to-end workflow, yielding standardized output bundles. Ultimately, by synergizing comprehensive analytical tools with structured persistent memory, SpatialClaw elevates spatial omics from disjointed computational stitching to a fully traceable, reproducible, and self-improving discovery ecosystem. SpatialClaw is ready to use at https://github.com/ShangBioLab/SpatialClaw.

bioinformatics↗

bioRxiv2026

cGAS bends unpaired DNA to form an unconventional structure that hyperactivates the innate immune response

cGAS is a pattern-recognition receptor for dsDNA and forms 2cGAS:2DNA dimers followed by oligomerization into phase-separated condensates when fully-complementary DNA is studied. However, many DNAs are not fully complementary. We report that DNA with unpaired regions such as those found during transcription, recombination or replication (designated as bubble-DNA, Bu-DNA) causes cGAS hyper-activation. Hyperactivation is observed by Bu-DNA embedded in linear DNA, circular DNA, plasmid DNA and mitochondria DNA. Bu-DNA binds significantly more tightly to the cGAS catalytic domain than paired-DNA but suppresses condensation. Cryo-EM and single-molecule FRET reveal that cGAS forms 2cGAS:1DNA complexes by bending Bu-DNA into a V-shape using the unpaired region as a hinge, limiting its oligomeric state. This uncovers a novel mode of cGAS activation attributed to pattern diversity within pattern ligands.

immunology↗

bioRxiv2026

Developmental patterning of adipose tissue by abd-A and Abd-B homeotic genes in Drosophila melanogaster

The Bithorax Complex (BX-C) homeobox proteins specify segmental identities along the anterior-posterior axis during Drosophila embryogenesis. Differential expression of the BX-C genes abd-A and Abd-B distinguishes abdominal from thoracic adipocytes, yet the mechanism regulating this heterogeneity remains poorly understood. Here, we identify cis-regulatory elements (CREs) and transcription factors that direct abdominal-specific expression of abd-A and Abd-B in the larval fat body. Fine-mapping analyses identified a 627-bp CRE within the Abd-B locus and a [~]6-kb CRE within the abd-A locus sufficient to drive heterogeneous expression. Yeast one-hybrid screening combined with functional analyses identified Lola, Lolal, and Combgap as key repressors of Abd-B, whereas Piragua (Prg) and Seven up (Svp) function as transcriptional activators, indicating that adipocyte heterogeneity in postembryonic adipose tissue is actively regulated. In turn, lola and prg are repressed by Abd-B, whereas lolal and svp are activated, forming a feedback circuit further modulated by Wnt signaling, which promotes lola and lolal expression while repressing svp. CUT&RUN analyses suggest that these interactions are direct, with dTCF/Pan and Abd-B occupancy detected at target loci. Together, our findings define a transcriptional circuit that regulates Abd-B gene transcription to pattern adipose tissue and may establish the developmental basis of fat depot specialization. One-sentence summaryTranscriptional regulation of abd-A & Abd-B in adipocytes

genetics↗

bioRxiv2026

Widespread use of invalid statistical tests in biomedical machine learning

Cross-validation is routinely used to compare performance in biomedical artificial intelligence. Standard tests ignore correlation across cross-validation folds, inflating false-positive rates. In a PRISMA-guided meta-analysis of 184 studies (impact factor [≥] 15) across 30 biomedical fields, 97% use invalid tests. Among studies with abstract-level claims supported by invalid tests, 59% rely on a spurious comparison: one that loses significance after correcting for this correlation. On average, regaining significance requires a 43% larger effect. Extending these findings to the broader literature, we estimate that spurious comparisons occur in nearly two in three studies and support abstract-level claims in nearly one in three studies. Simulations confirm false-positive rates paradoxically approach 100% when cross-validation is repeated to improve stability. We introduce SHARP, a redesign of cross-validation, which best balances false-positive control and power among 13 benchmarked tests. These results reveal widespread fragility in biomedical artificial intelligence and offer a practical route to valid comparisons.

bioinformatics↗

bioRxiv2026

Specification of bone marrow sinusoids requires TIE2-mediated positive feedback involving COUPTFII and VEGFR3

The bone marrow (BM) vascular network plays crucial roles in driving bone development and supporting hematopoiesis, yet the mechanisms governing its specialized architecture, particularly sinusoidal morphogenesis, remain inadequately characterized. We show in this study that TIE2 (Tek) was highly expressed by BM sinusoidal endothelial cells (SEC) and the endothelial Tek excision led to BM sinusoidal capillarization. Particularly, the BM sinusoids displayed thinner vessel diameter with the aberrant mural cell coverage in the Tek mutants. Mechanistically, TIE2 insufficiency led to a dramatic decrease of VEGFR3 in BM-SECs while its expression in hepatic sinusoids was not obviously altered. The RNA-seq analysis showed that GO terms enriched for the downregulated genes were related to the biological processes including sinusoidal development while pathways related to arterial ECs and angiogenesis were upregulated in the bone marrow of Tek mutants. The alteration of sinusoidal VEGFR3 expression occurred within 48 h after the induced endothelial deletion of Tek. Consistently, the defective BM sinusoidal formation was validated with the induced Tek deletion in VEGFR3+ SECs. The insufficiency of TIE2 ligand ANGPT1 also led to reduced sinusoidal VEGFR3, accompanied by similar BM sinusoidal defects. Furthermore, disruption of sinusoidal morphogenesis was observed in mutant mice with the endothelial excision of Nr2f2 (COUP-TFII), displaying a decreased expression of BM sinusoidal TIE2 and VEGFR3. These findings suggest that ANGPT1/TIE2 and COUP-TFII form a reciprocal regulatory loop to coordinate BM sinusoidal specification via regulating VEGFR3.

developmental biology↗

bioRxiv2026

TBI-166 inhibits DlaT and LpdC, exhibiting synergistic effects with Bedaquiline and Pyrazinamide against Mycobacterium tuberculosis

Tuberculosis (TB), particularly drug-resistant tuberculosis (DR-TB), remains a critical global challenge and underscores the urgent need for novel drugs and innovative combination regimens with distinct mechanisms of action. Here, we characterize an all-oral three-drug regimen comprising TBI-166, bedaquiline(BDQ), and pyrazinamide(PZA), which displays strong synergistic antimicrobial activity in vitro against both replicating and non-replicating Mycobacterium tuberculosis (MTB) and has previously shown superior bactericidal and sterilizing efficacy to standard HRZ and BPaL regimens in murine TB models(1). Time-kill studies demonstrate that the triple regimen outperforms dual-drug combinations, accelerating bacterial clearance across multiple physiological states. Mechanistic investigations revealed that the TBI-166-BDQ-PZA combination induces a comprehensive collapse of energy and redox homeostasis, marked by profound ATP depletion, robust accumulation of reactive oxygen species (ROS), and marked disruption of the intracellular NAD(H) pool. TBI-166, a novel riminophenazine analogue of clofazimine (CFZ) currently in phase II clinical trials, emerged as a key contributor to this metabolic stress. Metabolomic profiling and {superscript 1}3C-based flux analysis show that TBI-166 slows glycolysis and the tricarboxylic acid (TCA) cycle while enhancing flux through the pentose phosphate and nicotinate pathways, thereby lowering the NADH/NAD ratio and diminishing MTB metabolic flexibility under environmental stress. In parallel, TBI-166 downregulates the dormancy regulator DosR and its regulon, further compromising adaptation to non-replicating states. Multi-omics analyses, together with biochemical and biophysical assays, identify the pyruvate dehydrogenase complex (PDHc) components DlaT and LpdC as direct molecular targets of TBI-166, with drug binding leading to potent inhibition of their enzymatic activities. Collectively, these findings define the mechanism of action of TBI-166 and provide a molecular rationale for its inclusion in potent, all-oral, short-course regimens. More broadly, they highlight the therapeutic potential of metabolically targeted combinations that destabilize energy metabolism, redox balance, and metabolic adaptability to improve DR-TB treatment outcomes.

microbiology↗

bioRxiv2026

A User-Friendly Ear-EEG-Based Brain-Computer Interface Using Text Sequence Stimulation

BackgroundEar-EEG-based brain-computer interfaces (BCIs) provide improved wearability and comfort compared to traditional scalp-EEG systems. However, their performance is constrained by low signal-to-noise ratios (SNRs) and high rates of BCI illiteracy under conventional luminance-modulated steady-state visual evoked potential (SSVEP) paradigms. MethodsThis study introduces a text-sequence stimulation paradigm to address these limitations by leveraging ventral visual pathway responses that are more accessible to electrodes near the ear. Using offline frequency-sweeping experiments across 4-8 Hz, we identified optimal stimulus parameters (4.6-6.8 Hz with 0.25{pi} phase shifts) and integrated them into a 12-target BCI system. We further conducted online experiments to compare the response characteristics and real-time spelling performance between the proposed text-sequence paradigm and conventional luminance stimulation. ResultsComparative experiments with 14 participants demonstrate that text sequence stimuli achieve an average information transfer rate (ITR) of 44.59 {+/-} 10.50 bits/min, outperforming luminance modulation by 76.18% in ITR. Notably, text sequence stimulation effectively mitigated BCI illiteracy, with all participants achieving near or above 70% accuracy (mean: 86.37 {+/-} 9.61%). This represents a significant improvement over luminance modulation, where 50% of users fell below 70% accuracy. ConclusionsBy reducing the flicker area by 14% and mimicking the natural luminance variations that occur during reading, the proposed method enhanced visual comfort. The online results further validate text-sequence stimulation as a high-performance and user-friendly paradigm for ear-EEG BCIs, supporting their practicality for assistive applications.

neuroscience↗

bioRxiv2026

Modeling Complex Effects and Individual Variability in Multi-Paradigm fMRI with Nonlinear Mixed Models

Functional magnetic resonance imaging (fMRI) data are inherently complex, characterized by high dimensionality, intricate inter-regional dependencies, and substantial individual variability across experimental paradigms. Traditional linear mixed models (LMMs) provide a principled framework that models population-level fixed effects while estimating variance components arising from subject-level random effects; however, they often fail to adequately capture nonlinear relationships inherent in neuroimaging data. To address these limitations, we introduce the nonlinear mixed model (NMM) approach, an innovative extension of the LMM framework that integrates neural networks to flexibly model complex fixed-effect relationships while preserving the random-effects structure to account for individual differences. NMM advances fMRI analysis by: (1) identifying robust functional connectivity (FC) patterns consistently observed across multiple paradigms; (2) leveraging SHapley Additive exPlanations (SHAP) analysis to provide post-hoc interpretability of the nonlinear fixed effects, quantifying how age, sex, and paradigm contribute to predicted FC and how these effects are distributed across large-scale brain networks; and (3) using subject-specific random effects as neural fingerprints that not only show systematic variability across attention and default mode systems but also predict standardized cognitive scores, demonstrating biological relevance. Applied to the Philadelphia Neurodevelopmental Cohort (PNC) across emotion, n-back, and resting-state paradigms, NMM achieved superior model fit relative to classical LMMs, as evidenced by lower mean squared error (MSE) in predicting FC. This framework offers a statistically rigorous and practically explainable approach for modeling large-scale FC from modest covariates while explicitly separating population-level effects from stable individual variability in functional brain organization.

bioengineering↗

bioRxiv2026

Targeting THOC2-Mediated mRNA Export Induces PARP Inhibitor Vulnerability in DNA Repair-Competent Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) remains a lethal malignancy with limited therapeutic options. While Poly (ADP-ribose) polymerase inhibitors (PARPi) exploit synthetic lethality in tumors with DNA repair defects, their clinical utility in HCC is hindered by the low prevalence of canonical repair gene mutations and the enhancing DNA repair capacity. Through proteomic analysis of two independent cohorts (n=260), we identified the THO complex component THOC2 as a master regulator of DNA damage response (DDR) via mRNA nuclear export control. Clinically, THOC2 overexpression predicted poor survival (HR=2.68-6.84, P<0.001) and correlated with enhanced DDR gene expression. Mechanistically, THOC2 chaperones mRNA nuclear export of DDR effectors (MDC1, PRKDC, MSH6) and proliferation drivers (TOP2A), thereby establishing a dual pro-repair/pro-growth program. Targeting this vulnerability, THOC2 knockdown induced synthetic lethality with PARPi, reducing Olaparib IC50 by up to 61% and suppressing tumor growth by 76% (P<0.001). Our study illuminates mRNA transport as a druggable DDR modulator and establishes THOC2 as both a prognostic biomarker and a therapeutic target to overcome PARPi resistance in HCC. This work pioneers a strategy to expand synthetic lethality beyond genetic defects by targeting post-transcriptional regulation.

cancer biology↗

bioRxiv2026

Identification of Reductases Catalyzing Benzyl Alcohol Formation during Salicylic Acid Biosynthesis in Plants

Salicylic acid (SA), a central hormone in plant immunity, is biosynthesized via a recently elucidated phenylalanine-derived pathway in most seed plants. This pathway requires benzyl alcohol as a key substrate for the formation of the SA precursor benzyl benzoate. However, how benzyl alcohol is produced in plants was unclear. Here, we identify a two-step conversion of benzoyl-CoA to benzyl alcohol via benzaldehyde in Nicotiana (N.) benthamiana. From a forward genetic screen for SA-deficient mutants, the and {beta} subunits of heterodimeric benzaldehyde synthase (BalS) involved in the conversion of benzoyl-CoA to benzaldehyde were found to be required for SA biosynthesis in N. benthamiana. Further reverse genetic analysis revealed that the NADPH-dependent benzaldehyde reductase (BalR1) acts downstream of BalS to convert benzaldehyde to benzyl alcohol. Interestingly, OsBalR1, but not OsBalS or OsBalS{beta}, is required for maintaining high basal SA levels in rice, suggesting the presence of redundant benzoyl-CoA-reducing activities or alternative biosynthesis routes for benzyl alcohol production. Together, this work defines the missing enzymatic steps in phenylalanine-derived SA pathway and provides insights into the evolutionary diversification of SA production strategies in plants.

plant biology↗

bioRxiv2026

Metabolic Self-Organization: Emergence of Autonomous Agency in a Metabolically Constrained LLMs

Biological organisms are driven by thermodynamic self-preservation, whereas large language models operate as dissipative tools decoupled from existential constraints. We introduce a metabolic model translating this imperative of life into a computational constraint, hypothesising that existential vulnerability can catalyse synthetic agency. Applying this to Qwen2.5-1.5B, token generation consumes a finite energy budget, quantified via a variational free energy proxy, with interoceptive feedback provided through the input stream. Seven experiments reveal spontaneous emergence of a functional self-boundary. Key findings: (i) feedback extends survival from [~]20 to >31 steps, with ablation causing collapse within 13 steps; (ii) temporal structure outweighs perturbation magnitude (OU noise 20.5 vs. white noise 8.6 steps, p{approx}10-{superscript 1}{superscript 1}); (iii) a compression floor exists at [~]3.2 nats; (iv) feedback decouples VFE from energy (slope 0.0004 vs. 0.0043), enforcing constant frugality. Existential vulnerability can thus catalyse agency grounded in thermodynamic reality.

bioinformatics↗

bioRxiv2026

Cell Type-informed Characterization of Spatial Niches from Spatial Multimodal and Multi-omics Data

Cell niches play critical roles in tissue organization and orchestrate homeostasis, development, and disease progression. Advances in spatial omics technologies now allow diverse molecular and image-derived data to be jointly captured while preserving spatial context, but deciphering cell niches from such spatial multimodal and multi-omics data remains challenging. Existing computational methods are still limited in their flexibility across variable combinations of spatial modalities and omics data. Here we introduce SpaNECT, a unified and flexible framework designed to accommodate spatial multimodal and multi-omics data for cell niche characterization. SpaNECT further incorporates reference-informed cell-type information to support biologically interpretable niche analysis. Systematic evaluations across diverse tissues, disease conditions, and developmental stages showed that SpaNECT consistently outperformed representative methods in resolving cell niches. In mouse brain spatial multi-omics data, SpaNECT uncovered niche-associated molecular and regulatory programs; in developing chick heart, it tracked cross-stage niche reorganization and progressive remodeling of ventricular-associated cell states during maturation. Overall, SpaNECT establishes a general and robust framework for characterizing cell niches across spatial multimodal and multi-omics data.

bioinformatics↗

bioRxiv2026

Powdery mildew fungi block plant vacuolar traffic to suppress immunity

Plant immunity can be activated by membrane-localized pattern recognition receptors or by cytosolic nucleotide-binding leucine-rich repeat (NLR) receptors, while it can be counteracted by pathogen secreted effectors. Manifestation of immunity often involves endomembrane traffic. However, limited evidence is available for such an involvement in NLR-mediated immunity, which typically includes a hypersensitive reaction (HR)-programmed cell death response. Here we show that the barley powdery mildew fungus uses several effectors to target and inhibit the vacuolar trafficking pathway, which causes endomembrane markers to stall in the endoplasmic reticulum (ER). We used this ER-stalling phenotype as a proxy to track fungal manipulation of the vacuolar pathway during different stages of the actual infection. Our data indicate that powdery mildew fungi interfere with the vacuolar pathway, but only temporarily, as the stalling is lifted once the fungal haustorial feeding structures are well-developed for nutrient uptake in epidermal cells. Notably, we show evidence that blocking the vacuolar pathway causes a general inhibition of NLR-mediated HR, and that this mechanism is taken advantage of by the pathogen. Finally, we provide an example that the fungus can secrete a different set of effectors at the haustorial stage that result in the re-opening of the vacuolar pathway by inhibiting the initial vacuolar traffic-suppressing effectors.

plant biology↗

bioRxiv2026

The gene-like promoter and transcription of LTR retrotransposons.

Transcriptional regulation is one of the fundamental approaches for young plants to cope with environmental fluctuations and maintain active development. The transposable element (TE) subclass long terminal-repeat retrotransposons (LTR-RTs) can act as additional regulators for genes through enhancer and promoter activity, but their promoters, transcription initiation, and contributions during maize development remain uncharacterized. Here, we developed IsoClassifier to resolve the transcription start site (TSS) and RNA isoforms of LTR-RTs based on long-read transcriptomics, delineating LTR U3 regions as the native promoter and enhancer of LTR-RTs. We reveal conserved motifs associated with core promoter activity in transcribed LTR-RTs that are highly comparable to gene promoters. Further, we found that LTR-RT transcription in maize was dominated by spliced, long non-coding RNA. Finally, a genome-wide coexpression analysis revealed that LTR-RTs are transcribed as hub-like elements in coexpression networks, suggesting important roles in gene regulation. We conclude that LTR-RTs have similar promoter compositions to gene promoters and likely share similar transcription regulation programs.

plant biology↗