Biology subjects

Wei, H.

Publications and source records attributed to Wei, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Microbial Reductive Dechlorination of Hexachlorobutadiene by Dehalococcoides

Hexachlorobutadiene (HCBD), a persistent organic pollutant (POP), poses a significant threat to ecological environments and human health. While anaerobic microbial transformation is a promising remediation strategy, the specific microorganisms and metabolic mechanisms involved have remained poorly understood. This study demonstrates the successful enrichment of an anaerobic microbial consortium from river sediment, with lactate as an electron donor, capable of transforming HCBD. Within 240 days, 62.5 mol of HCBD was sequentially dechlorinated through pentachlorobutadiene (PCBD), tetrachlorobutadiene (TeCBD), trichlorobutadiene (TCBD), and dichlorobutadiene (DCBD) to chlorobutadiene (CBD). Co-amendment with HCBD and trichloroethene (TCE) resulted in complete removal of both compounds. 16S rRNA gene sequencing and quantitative PCR showed enrichment of Dehalococcoides, linking its population growth to HCBD and TCE dechlorination. This study demonstrates that Dehalococcoides growth was associated with HCBD transformation in the enrichment cultures, broadens our understanding of the metabolic capabilities of Dehalococcoides, and identifies a candidate gene for this important environmental process, offering valuable insights for the bioremediation of sites contaminated with HCBD.

microbiology↗

bioRxiv2026

The FKBP42, TWISTED DWARF1, prioritizes auxin over brassinosteroidtransport by peptidyl-prolyl cis-trans isomerization of ABCB1

The ATP-binding cassette (ABC) transporter ABCB1 transports both auxins and the brassinosteroid brassinolide (BL). ABCB1-mediated auxin (IAA) transport depends on interaction with the FKBP42 protein TWISTED DWARF1 (TWD1), yet the mechanism underlying substrate selectivity remains unclear. Here, we confirm dual IAA and BL transport by ABCB1 and show that the two substrates compete for ABCB1-mediated transport. We demonstrate that a conserved proline residue (P1008) is required for IAA, but not BL, transport. Furthermore, we identify TWD1 as a calmodulin-activated peptidyl-prolyl cis-trans isomerase (PPIase) that selectively enhances IAA, but not BL, transport through isomerization of the E1007-P1008 peptide bond. Loss of TWD1 PPIase activity abolishes ABCB1-mediated IAA export without affecting BL transport, revealing a regulatory mechanism that prioritizes auxin over brassinosteroid transport. Cryo-EM, molecular docking, and molecular dynamics simulations of wild-type ABCB1 and the ABCB1P1008G variant suggest that the P1008 loop mediates long-range communication between the nucleotide-binding domain surface and the substrate-binding pocket, thereby providing a structural mechanism by which TWD1 modulates substrate specificity. In summary, our findings establish the structural basis of ABCB1 substrate selectivity and uncover a post-translational mechanism that selectively regulates auxin transport while preserving brassinosteroid transport. One Sentence SummaryTWD1 prioritizes ABCB1-mediated auxin over brassinosteroid transport

biochemistry↗

bioRxiv2026

Complete Mutagenesis of the Genome and Proteome of {Phi}X174

The bacteriophage {Phi}X174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the {Phi}X174 genome and every amino acid in the proteome. In total, half of nucleotide and >60% of amino acid changes impair fitness. However, this varies substantially across proteins and non-coding regions. Surprisingly, the most important mechanistic cause of reduced fitness is disruption of protein interaction interfaces, accounting for nearly half of detrimental protein variants. A further one quarter of damaging variants disrupt protein cores but one in four lack a mechanistic explanation. Mutational effects are only moderately-well predicted by state-of-the-art artificial intelligence models, but, combined with structural modelling, provide mechanistic hypotheses and insights into the DNA replication machinery. This complete mutagenesis of a biological system quantifies the limits of our current understanding of, and ability to predict, molecular biology.

genomics↗

bioRxiv2026

Selective repurposing of the eukaryotic DNA replication machinery by a plant virus

Eukaryotic DNA viruses that replicate in the nucleus often exploit components of the host DNA replication machinery for genome replication. Geminiviruses, causal agents of devastating crop diseases worldwide, strictly depend on host factors to replicate their circular single-stranded (ss) DNA genomes, with only a single virus-encoded protein, Rep, required for this process. Rep recruits host replication proteins to the viral genome and catalyzes nicking and ligation at the initiation and termination sites of rolling-circle replication. Despite the reliance of geminiviral replication on plant proteins, the composition of the viral replisome remains largely unknown. Here, we use TurboID-based proximity labeling to identify plant proteins in the vicinity of the Rep proteins from the geminiviruses tomato yellow leaf curl virus (TYLCV) and abutilon mosaic virus (AbMV) during infection. Combining virus-induced gene silencing, infection assays, and chromatin immunoprecipitation, we identify host DNA replication-related factors required for viral genome replication and likely components of the viral replisome. Our results indicate that geminiviruses and related eukaryotic ssDNA viruses selectively repurpose components of the eukaryotic replication fork to support rolling-circle replication, and suggest that they follow a leading-strand replication mode while utilizing the lagging-strand DNA polymerase {delta}. These findings shed light on the molecular mechanism of geminiviral DNA replication and identify potential targets for engineering antiviral resistance in crops.

plant biology↗

bioRxiv2026

SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics

Spatially resolved transcriptomic (SRT) data requires spatial domain identification to enable tissue microenvironment-specific downstream analyses. Here we present SPEAK (Spatial Prompting with Expert-Aligned Knowledge), a large language model (LLM)-based method to identify spatial domains from SRT data by taking advantage of the prior knowledge from both LLM and human experts. SPEAK constructs a spatial context prompt for each cell/spot based on cell types and marker genes of its neighboring cells, enabling zero-shot inference, expert-guided fine-tuning, and prototype updating through two-stage prompting. Applications to STARmap, Visium, MERFISH and Xenium datasets showed advantages of SPEAK over existing spatial domain identification methods in domain prediction accuracy, robustness to limited prior knowledge, biological interpretability, and capacity for efficient expert-guided fine-tuning with generalizability to other tissue sections.

bioinformatics↗

bioRxiv2026

Genetic suppression of myeloid receptor Clec7a attenuates microglia neuroinflammation and promotes microglial phagocytosis to delay disease progression in ALS models

Microglial activation has been closely associated with accelerated ALS disease progression. However, specific microglial pathways that regulate microglial activation and ALS disease progression remain limitedly understood. Here, we determined the role of Clec7a (or Dectin-1), a core signature gene of disease-associated microglia (DAM) in ALS, in regulating microglial activation and ALS disease progression. Our spinal cord scRNA-Seq results found that Clec7a deficiency specifically attenuated microglial neuroimmune gene expression in SOD1G93A mice and human ALS. In addition, in vivo two-photon imaging of human (h) TDP43 phagocytosis by microglia in the cortex showed that Clec7a deficiency promotes microglial phagocytosis of pathological hTDP43 by enhancing microglial process dynamics. Subsequent survival analysis further showed that selective deletion of Clec7a in microglia mitigates motor neuron degeneration and delays disease progression in SOD1G93A ALS mice. Together, our results establish that Clec7a is a key regulator in shaping disease microglial functions and promotes disease progression in ALS.

neuroscience↗

bioRxiv2026

Karrikin and strigolactone signalling affect pattern-triggered immunity and resistance to specific pathogens

Hormone signalling is important for plant adaptation to biotic stress. Karrikins (KARs), smoke-derived compounds, and strigolactones (SLs), endogenous plant hormones, are families of butenolide mole-cules, sharing a convergent perception and signalling pathway to regulate a plethora of developmental processes and plant-symbiont relationships. Perception of KARs and SLs is mediated by the /{beta}-hydro-lase KARRIKIN INSENSITIVE 2 (KAI2) and DWARF14 (D14), respectively, each resulting in the for-mation of an E3 ubiquitin ligase complex with the F-Box protein MORE AXILLIARY GROWTH 2 (MAX2) to target transcriptional repressors of the SUPPRESSOR OF MAX2 (SMAX)/SMAX-LIKE (SMXL) family for degradation. Most likely, KAI2 additionally perceives a still elusive endogenous ligand (KAI2-ligand, KL). Recent reports suggest a role of KL/SL signalling in plant immunity, but how these pathways are involved in defence, while balancing appropriate symbiont interactions remains largely unknown. Here, we report that KL and SL signalling quantitatively modulate plant immune responses and pathogen re-sistance. In Arabidopsis thaliana (hereafter Arabidopsis), disrupting or de-repressing KL or SL signalling affects plant susceptibility to a variety of plant pathogens. Furthermore, we describe a previously un-known role for KL and SL signalling in modulating pattern-triggered immunity (PTI). Interfering with KL and SL perception in Arabidopsis had similar effects on microbe-associated molecular pattern (MAMP)-triggered reactive oxygen species production, but transcriptomic profiling suggests a predominant role for KL signalling in regulating the extent of PTI. Importantly, KAI2- and D14-mediated regulation of MAMP-triggered ROS production extends to Lotus japonicus and, in the case of KAI2, to Nicotiana benthamiana, indicating conserved immuno-modulatory roles across dicotyledonous lineages. Together our data identify KL and SL signalling, with a predominant role for the KL pathway, as a conserved modulatory layer of plant immunity and provides a framework for understanding how developmental pathways intersect with immune regulation.

plant biology↗

bioRxiv2026

Engineering Dual-Target Chimeric Lysins for Synergistic Eradication of Porphyromonas gingivalis

Periodontitis is a chronic inflammatory disease driven by complex subgingival multispecies biofilms, in which Porphyromonas gingivalis plays a central role in coordinating microbial interactions. Together with host-associated factors, these microbial communities create dual constraints that limit antimicrobial efficacy. In this study, we engineered a library of recombinant lysins by fusing membrane-destabilizing peptides to the periodontal pathogen-derived lysin LysPd078 and identified four optimized variants (PlyPd06, PlyPd19, PlyPd27, and PlyPd44) with enhanced salt tolerance, environmental stability, and bactericidal activity. In a clinically derived polymicrobial oral biofilm, PlyPd44 at only 25 g/mL eradicated 96.6% of P. gingivalis. In a humanized oral microbiota mouse model of periodontitis, selected PlyPds significantly reduced inflammation and inhibited alveolar bone loss compared with LysPd078 and minocycline. Collectively, these results establish membrane-destabilizing peptide-enabled lysins as a promising platform for developing microenvironment-adapted precision antimicrobials for periodontitis.

microbiology↗

bioRxiv2026

Decoding Single-Cell Omics of Perturbation Responses Using DeSCOPE

Deciphering cellular responses to genetic perturbations is fundamental to modeling gene regulatory networks and understanding mechanisms that change cellular phenotypes. However, current computational approaches often fail to outperform simple baseline models, highlighting a critical bottleneck in their generalizability and robustness. Here, we present DeSCOPE, a lightweight conditional variational autoencoder framework for predicting genetic perturbation responses spanning transcriptomic, epigenomic, and broader multi-modal landscapes. We systematically benchmarked DeSCOPE across diverse datasets under two challenging out-of-distribution settings: unseen genes and unseen cell types. DeSCOPE uniquely surpasses simple baselines in the unseen gene scenario, and achieves substantially improved performance for unseen cell types while requiring fine-tuning with far fewer perturbed genes. Finally, DeSCOPE demonstrates superior performance in predicting combinatorial multi-gene perturbations. Overall, DeSCOPE serves as a versatile multi-modal virtual cell model that can effectively guide the design of therapeutic targets that change cellular phenotypes. DeSCOPE is available at https://github.com/wanglabtongji/DeSCOPE.

bioinformatics↗

bioRxiv2026

Structure-based similarity network accelerates the discovery of lysins as oral microbiome modulators targeting periodontal pathogens

Microorganisms significantly influence human health, and dysbiosis of the oral microbiome plays a critical role in the development and progression of both oral and systemic diseases. This highlights the urgent need for novel therapeutics targeting specific pathogens. Here, we presented a structure-based pipeline to efficiently identify potential phage-derived periodontal lysins (LysPds) from nearly one million proteins. We predicted the structures of candidate lysins using AlphaFold2 and developed an innovative structure-based similarity network to classify them into distinct clusters, each with unique functional properties. A systematic characterization of 16 representative LysPds from 11 superfamilies revealed that over 90% demonstrated potent antibacterial activity against key periodontal pathogens. Among these, LysPd078 was identified as a promising preclinical drug candidate, effectively reconfiguring microbiome communities while demonstrating significant efficacy and safety in mouse models of periodontitis and calvarial infection. Our findings highlight the effectiveness of structure-based similarity networks in exploring vast protein spaces and underscore the potential of LysPd078 as a targeted modulating agent for the oral microbiome.

microbiology↗

bioRxiv2026

Glia generate distinct visual processing centres by locally inhibiting ERK activity in an optic lobe neuroepithelium

Epithelial patterning is fundamental to organ development. Extensive work has focused on how neuroepithelia are patterned to generate diverse progenitors, yet how a single neuroepithelium is partitioned to produce distinct processing centres is poorly understood. Here, we focus on the Drosophila outer proliferation centre neuroepithelium, which generates the medulla and lamina visual processing centres. Medulla neuroblasts are produced by a proneural wave that initiates at the medial margin of the neuroepithelium and moves laterally propagated by EGFR-ERK signalling, whereas lamina precursors arise at the lateral neuroepithelial margin and have been proposed to require photoreceptor-derived Hedgehog. Here, we show that Hedgehog signalling is dispensable for lamina precursor specification but instead promotes their survival. In contrast, suppressing ERK and apoptosis together is sufficient to drive ectopic lamina precursor development. We find that cortex glia secrete the EGF antagonist Argos, which accumulates at the lateral neuroepithelium, thus repressing ERK activity locally. Together, our findings reveal a glia-mediated, extrinsic patterning mechanism that suppresses EGFR-ERK signalling in the lateral neuroepithelium, protecting these cells from the proneural wave and instructing lamina over medulla fate. Summary statementGlial cells locally control ERK signalling to partition a developing tissue, enabling distinct structures to arise from a common neuroepithelium.

developmental biology↗

bioRxiv2026

Molecular Glue-Induced Homodimerization Drives Targeted CRBN Autodegradation

Molecular glue degraders (MGDs) offer a sophisticated, proximity-based approach to protein modulation. In this study, we introduce LJY-3-60, a novel proximity-inducing agent that unexpectedly triggers the potent and selective autodegradation of CRBN. Evidence from CRISPR-Cas9 screening and IP-MS reveals that this degradation process is strictly governed by the intrinsic CRL4CRBN machinery, independent of any extrinsic E3 recruitment. Through a combination of cellular and biophysical characterizations, we demonstrate that LJY-3-60 acts as a molecular bridge to template CRBN homodimerization. This mechanism is unequivocally elucidated by the atomic-resolution co-crystal structure of the CRBNMidi-LJY-3-60 complex. The structure explicitly delineates the homodimerization interface, revealing how the ligand reorganizes the protein surface to stabilize a non-canonical architecture that drives trans-autoubiquitination and subsequent proteasomal degradation. Furthermore, LJY-3-60 serves as a highly effective, controllable off-switch to mitigate PROTAC-induced toxicity. Ultimately, this work delivers a robust chemical tool for modulating CRBN stability. By demonstrating how a small molecule can functionally mimic an endogenous E3 substrates degron to catalyse targeted autodegradation, this study establishes a rational structural framework for designing the next generation of self-destructive modulators in targeted protein degradation (TPD) therapeutics.

biochemistry↗

bioRxiv2026

Alternative splicing expands the functional portfolio of a plant virus to control the viral cycle

Viruses frequently have limited coding space, yet efficiently manipulate complex hosts by deploying intricate, often poorly understood strategies. Geminiviruses, devastating plant pathogens with small single-stranded (ss) DNA genomes, replicate in the nucleus aided by the viral replication-associated protein (Rep), the most conserved protein within this family and related ssDNA viruses. Rep initiates viral DNA replication and represses its own promoter to regulate the infection cycle. The molecular mechanisms enabling this dual functionality are so far unknown. Here, we show that the geminivirus tomato yellow leaf curl virus (TYLCV) exploits the host spliceosome to produce novel Rep splice variants. Splicing generates Rep isoforms lacking the central oligomerization domain that cannot initiate replication but strongly repress the Rep promoter. Conversely, Rep mutants deficient in splicing promote replication but fail to repress transcription. Reduced Rep splicing interferes with the viral gene expression hierarchy and decreases infectivity. Our findings therefore reveal a previously unrecognized viral strategy in which alternative splicing produces functionally specialized viral protein isoforms, providing a mechanistic explanation for the dual role of Rep in viral replication and gene regulation. Splicing events with potentially similar functional consequences in related viruses suggest that this strategy may have convergently evolved across diverse viral lineages infecting different domains of life.

plant biology↗

bioRxiv2026

Large-scale quantum computing framework enhances drug discovery in multiple stages

Coherent Ising machines (CIMs) excel at solving large-scale combinational optimization problems (COPs), but their insufficient long-term stability has hindered their applications in compute-intensive tasks like computer-aided drug discovery (CADD). By improving fiber vibration isolation and temperature control system, we have implemented a 2000-node CIM named QBoson-CPQC-3Gen achieving stable solutions over one hour on large-scale COPs. Graph-based encoding schemes were further introduced to realize a CIM-based CADD workflow including allosteric site detection, protein-peptide docking and intermolecular similarity calculation. CIM-based methods demonstrated superior speed and accuracy than heuristic algorithms. Especially, QBoson-CPQC-3Gen identified 2 novel druggable sites and bioactive compounds for 6 targets, which were further validated in vitro, in-cell and by crystal structures. Our contributions established a quantum-computing framework for multi-stage drug discovery, representing a significant advancement in both quantum computing applications and pharmaceutical research.

bioinformatics↗

bioRxiv2026

Characterization of the C4 proteins encoded by okra-infecting geminiviruses in India

Okra (bhendi) is a widely cultivated food crop in warm regions of the world, with India contributing approximately 60% of global production. However, okra cultivation in India is severely constrained by viral diseases, among which infections caused by the geminiviruses bhendi yellow vein mosaic virus (BYVMV) and okra enation leaf curl virus (OELCuV), in association with their satellites, represent major limitations to crop productivity. In recent years, the geminivirus-encoded C4 protein has emerged as a key pathogenicity determinant in this viral family, with functions that include suppression of multiple layers of plant antiviral defence and induction of disease symptoms. Here, we comparatively characterize the C4 proteins of BYVMV and OELCuV by determining their targeting signals and subcellular localization, and by assessing their ability to induce developmental abnormalities and suppress the cell-to-cell spread of RNA silencing. Our results reveal that the two C4 proteins display distinct subcellular localization patterns, yet both are capable of inducing developmental alterations, likely through different mechanisms, and of suppressing the intercellular spread of RNA silencing, possibly via interaction with a common host factor. Together, these findings suggest that C4 might be a critical virulence factor in okra-infecting geminiviruses and act as a symptom determinant. The C4 proteins encoded by BYVMV and OELCuV therefore emerge as promising targets for the development of antiviral management strategies in okra.

plant biology↗

bioRxiv2025

Transport of endo-β-mannosidase AtEBM from cytoplasm to the vacuole through autophagy pathway in Arabidopsis

Autophagy is a conserved eukaryotic intracellular degradation pathway that exhibits specialized forms, such as the biosynthetic cytoplasm-to-vacuole targeting (Cvt) pathway in yeast. This pathway selectively delivers several hydrolase precursors to the vacuole. While the core autophagy machinery is highly conserved between yeast and plants, the existence of a similar Cvt-like pathway for vacuolar hydrolase trafficking in plants remains unclear. Here, we found that Arabidopsis thaliana endo-{beta}-mannosidase (AtEBM), a glycosidase involved in degrading vacuolar N-glycans released from glycoproteins, is selectively transported to the vacuole via autophagy. Further analyses revealed that AtEBM directly interacts with the core autophagy protein ATG8 through an ATG8-interacting motif (AIM). This interaction is essential for sequestering AtEBM into autophagosomes. Remarkably, the AIM is conserved among EBM orthologs across the green plant lineage. In addition, several phenotypic studies showed that atebm mutants generated through CRISPR-Cas9 editing did not exhibit autophagy defects, including early senescence and hypersensitivity to nutrient starvation, but rather had reduced fecundity. Thus, these findings reveal a Cvt-like pathway in plants that fulfills a biosynthetic role by selectively delivering the glycosidase AtEBM to the vacuole.

cell biology↗

bioRxiv2025

GBoost-CTL: A novel method in multi-tissue transcriptome-wide associations studies in cross-tissue learner incorporating GWAS information

Genome-wide association studies (GWAS) have uncovered numerous genetic variants linked to complex human diseases, yet linking these variants to transcripts and tissues that drive pathology remains difficult. Multi-tissue transcriptome-wide association studies (TWAS) offer a powerful bridge, but existing analytical methods have some limitations, either by discarding important signals by separately analyzing and then aggregating results across tissues, implying imputation models in individual tissues, or fusing them with weights that ignore how much GWAS signal each tissue actually carries. Therefore, most of the existing methods do not work uniformly across different GWAS cohorts. Here, we propose GBoost-CTL - a GWAS-boosted cross-tissue learner that can overcome those aforementioned limitations. The method starts with any collection of single-tissue learners (STLs), allowing investigators to choose the most suitable imputation engine for each tissue. It then (i) allocates weights according to each STLs out-of-sample predictive accuracy and (ii) refines those weights incorporating the GWAS-derived information, so that informative tissues are automatically up-weighted while uninformative tissues are down-weighted. This dual weighting strategy lets GBoost CTL adapt to fully shared, partially shared, or highly tissue-specific regulatory architectures while preserving nominal type I error control and delivering substantially higher power than existing linear or covariance-based methods. Through extensive simulation, we have found that this dual weighting strategy lets GBoost-CTL adapt to fully shared, partially shared, or highly tissue-specific regulatory architectures while preserving nominal type I error control and delivering substantially higher power than existing linear or covariance-based methods. When applied to real data, GBoost-CTL consistently outperformed some existing multi-tissue TWAS methods (e.g., TWAS-CTL, UTMOST and PrediXcan) by identifying a greater number of disease-associated genes with more stringent p-values. Given its modular design, computational scalability, and demonstrable gains in discovery power, we believe that GBoost-CTL offers a practical tool for the analysis of multi-tissue TWAS.

bioinformatics↗

bioRxiv2025

Mechanical Disturbance of Trichomes Enhances Cd2+ Uptake via Malate-Mediated Stomatal Opening in Arabidopsis

Phytoremediation of cadmium-contaminated soils relies on efficient metal uptake and translocation in plants. We previously found that gentle mechanical stimulation of non-glandular trichomes by brushing significantly enhances shoot Cd{superscript 2} accumulation in Arabidopsis thaliana, although the underlying physiological mechanism remained unclear. Here, we demonstrate that trichome brushing specifically induces stomatal opening, elevates transpiration, and promotes Cd{superscript 2} uptake, as evidenced by measurements of stomatal aperture, stomatal conductance, transpiration rate, and Cd{superscript 2} concentration in wild-type and mutant leaves. These responses are absent in the glabrous gl1-1 mutant and are not elicited by brushing epidermal pavement cells, indicating a trichome-specific mechanosensory pathway. Mechanistically, this pathway requires MPK3/MPK6 activity and employs malic acid as a key regulator of stomatal aperture, functioning independently of canonical ABA signaling. Our findings uncover a previously unrecognized trichome-to-stomatal signaling cascade that links trichome mechanostimulation to enhanced heavy metal accumulation.

plant biology↗