Biology subjects

Zhang, R.

Publications and source records attributed to Zhang, R..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of freely swimming zebrafish larvae

Understanding the behavioral and morphological dynamics of moving model organisms like the zebrafish larvae requires accurate, high-throughput 3D analysis. However, traditional single-view 2D video tracking fails to capture the full scope of natural 3D movements and postural dynamics. Here, we present a novel high-throughput 24-camera array microscope with a co-designed "mirrored well plate" that allows for snapshot imaging of up to 48 wells over a 118 mm x 82 mm field of view from two orthogonal directions (i.e., a top-view and side-view). Accurate 3D position estimation and tracking is achieved with an efficient machine learning algorithm that scales well to high-throughput measurements. The proposed approach automates parallelized 3D model organism behavioral analysis, providing 3D skeletal tracking, swim bladder morphological dynamics, and kinematics of up to 48 swimming zebrafish larvae at up to several hundred frames per second. The result is an efficient and scalable solution for high-throughput 3D behavioral studies with broad compatibility with standard workflows across laboratories and procedures working with pharmacology, toxicology, and neuroscience.

animal behavior and cognition↗

bioRxiv2025

Homodimerized Arpins: Binding to Arp2/3 Complexes with Positive Synergy to Inhibit Lamellipodia-Dependent Tumor Metastasis

The Arp2/3 complex is a central regulator of actin polymerization dynamics and cancer cell motility, with its dysregulation implicated in metastasis and therapeutic resistance. Despite its therapeutic potential, targeting Arp2/3 remains challenging due to the lack of precise molecular insights into endogenous inhibitors. Arpin, a lamellipodia-localized Arp2/3 inhibitor, has emerged as a critical modulator of cancer migration; however, the structural and mechanistic basis of its inhibitory function remains unresolved. Here, we report the 1.65-[A] crystal structure of Arpins N-terminal globular domain, revealing a unique structural fold distinct from all known Arp2/3-binding factors. Structural and biophysical analyses demonstrate that Arpin forms homodimers via a conserved interface, which is essential for cooperative inhibition of Arp2/3-dependent actin polymerization. Functional studies in cancer models reveal that Arpin homodimerization potently suppresses lamellipodia-driven migration and invasion, effects further enhanced by engineered dimeric constructs or artificially designed dual-tailed peptides. These findings elucidate a structural basis for Arpin-mediated suppression of cancer cell motility and identify homodimeric cooperativity as a druggable mechanism for targeting metastatic progression. Our work provides a molecular framework for designing Arpin-inspired inhibitors to counteract therapeutic resistance and metastasis in cancers reliant on Arp2/3-driven actin dynamics.

cancer biology↗

bioRxiv2025

Development of a replication-defective MPXV platform for fundamental and therapeutic research

The recent global outbreaks of mpox highlight the urgent need for both fundamental research and antiviral development. However, studying monkeypox virus (MPXV), with its large and complex genome, remains challenging due to the requirement for high-containment facilities. Here, we describe a novel strategy for de novo assembly of MPXV clade IIb genomes in bacterial artificial chromosomes using transformation-associated recombination cloning. Leveraging CRISPR-Cas9 and Lambda Red recombination, we engineered replication-defective MPXV particles with dual deletions of OPG96 (M2R) and OPG158 (A32.5L)--genes essential for virion assembly, that are capable of recapitulating key stages of the viral life cycle. Our work demonstrates the utility of replication-defective MPXV particles as a reliable platform for high-throughput antiviral discovery, offering significant advantages for both fundamental virology studies and therapeutic development against orthopoxviruses.

microbiology↗

bioRxiv2025

Metabolite Interactions Mediate Beneficial Alliances Between Bacillus and Trichoderma for Effective Fusarium Wilt Control

Bacteria-Fungi Interactions play a crucial role in soil nutrient cycling and plant disease suppression. Bacillus and Trichoderma exhibit antagonism when inoculated on laboratory media, global soil sample analysis reveals a positive correlation between these two genera in addition to enhanced plant-pathogen Fusarium oxysporum (FOC) suppression and plant growth promotion. Here, we depict a complexity of interactions in a cross-kingdom consortia of Bacillus velezensis and Trichoderma guizhouense. Transcriptomic profiling revealed that in the presence of fungi, the key stress sigma factor of B. velezensis activates expression of biosynthetic genes for antimicrobial secondary metabolite production. Among these, surfactin induces T22azaphilone production in T. guizhouense that hinders oxidative stress. Both surfactin and T22azaphilone contribute to Bacillus and Trichoderma maintenance in soil in the presence of FOC. Finally, FOC-secreted fusaric acid temporarily inhibits B. velezensis growth while it is efficiently degraded by T. guizhouense. These metabolite-mediated interactions reveal how competing soil microorganisms could form effective alliances that ultimately enhance plant protection against soil-borne pathogens.

microbiology↗

bioRxiv2025

Structural insights into wiring specificity in the neuromuscular system through the Beat-Side complex

Nervous system assembly is guided by the actions of cell surface receptors. In Drosophila, members of the Beaten Path (Beat) and Sidestep (Side) protein families have been described as axon guidance receptor-cue pairs, in addition to roles in specifying synaptic connectivity in the optic lobe. To understand the molecular basis and specificity of Beat-Side interactions, we report here the first Beat-Side structure, Beat-Vc bound to Side-VI. The structure showed a binding topology similar to other neuronal immunoglobulin superfamily receptors, especially Nectins, SynCAMs, Dprs and DIPs, despite lack of established evolutionary relationships. Using a structure-based rational approach, we engineered and validated point mutations to break the binding between Beats and Sides. Using these mutant variants, we demonstrated in developing Drosophila larvae that the interaction between Beat-Ia and Side is required for establishing proper connectivity of motor neurons with muscles.

neuroscience↗

bioRxiv2025

Contrastive Learning-Enhanced Drug Metabolite Prediction Drives the Discovery of an Orally Bioavailable RSK4 Inhibitor for Esophageal Cancer

Drug metabolism liabilities are a major bottleneck in drug development, necessitating accurate metabolite prediction tools. While AI-driven methods have advanced, challenges remain in achieving high-precision, robustness, broad reaction coverage and seamless integration into the drug development workflow. To address this, we first constructed the most comprehensive human-specific drug metabolism database to date, encompassing 11,665 human metabolic reactions and 2,497 high-quality rules. Leveraging this resource, we developed ConMeter (Contrastive learning and feature interaction based Metabolic Reaction prediction), a novel model integrating chemical feature interaction and contrastive learning. ConMeter demonstrates significant improvements, achieving [~]80% accuracy in identifying at least one metabolite within the top 5 predictions and showing an average 25% relative enhancement in ranking true positives compared to state-of-the-art methods. The comprehensive database also expands the range of predictable metabolic reactions. To demonstrate the utility of ConMeter, we integrated it into a metabolite prediction-guided drug design strategy aimed at addressing the low oral bioavailability of a metabolically vulnerable RSK4 lead compound -- a pervasive issue among known RSK inhibitors. This strategy successfully yielded R636, a novel RSK4 inhibitor exhibiting remarkably improved bioavailability (a 63-fold increase, reaching 63% absolute bioavailability) while maintaining its potent activity. Notably, R636 showed favorable safety profile and significant anti-tumor efficacy against esophageal squamous cell carcinoma (ESCC) in vitro and in two distinct patient-derived xenograft (PDX) mouse models. This work introduces ConMeter as a powerful and practical tool for high-accuracy metabolite prediction, demonstrating its potential to accelerate lead optimization, exemplified by the discovery of R636 as a promising orally bioavailable candidate for ESCC.

cancer biology↗

bioRxiv2025

Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation

Hematopoietic stem and progenitor cells (HSPC) respond to infections, inflammation, and regenerative challenges using a collection of cellular and molecular mechanisms termed emergency myelopoiesis (EM) pathways. However, it remains unclear how various EM inducers regulate HSPCs using shared or distinct molecular mechanisms. Here, we generate a comprehensive and generalizable cell annotation method (HemaScribe) and a refined quantitative model of hematopoietic differentiation (HemaScape) using single cell RNA sequencing (scRNA-seq) of HSPCs, which we apply to a broad range of EM modalities. We uncover multiple strategies to enhance myelopoiesis acting at different levels of the HSPC hierarchy, which are associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based module of EM engagement across diverse inflammatory challenges, which informs outcome in adult and pediatric human acute myeloid leukemia. Collectively, our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration that have direct translational applications in disease contexts. HIGHLIGHTSO_LINew HemaScribe method for hematopoietic progenitor annotation in scRNA-seq datasets C_LIO_LIDifferent emergency myelopoiesis (EM) inducers act at distinct hematopoiesis levels C_LIO_LIUnique and shared transcriptional response modules enacted by different EM inducers C_LIO_LIA myeloid progenitor EM module informs outcome in acute myeloid leukemia C_LI eTOC BLURBSwann et al. conduct comparative analysis of single cell RNA sequencing data from multiple emergency myelopoiesis models, finding that different perturbations act at various levels of the hematopoietic hierarchy and recruit distinct sets of molecular mechanisms to enhance myelopoiesis. In particular, they identify a conserved myeloid progenitor-based activation module across multiple disease conditions, which informs outcome in human acute myeloid leukemia. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/656712v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@ffcd62org.highwire.dtl.DTLVardef@50eaeorg.highwire.dtl.DTLVardef@6df44org.highwire.dtl.DTLVardef@12bfacf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Promoting social connectedness through multi-person neurofeedback

Humans are inherently driven to build meaningful relationships, but attempts to socially connect with others are not always successful. This study investigates whether social connectedness can be improved by intentionally regulating inter-brain coupling, a neural correlate of successful social interactions. Using a multi-person neurofeedback system (i.e., a multi-brain computer interface), we showed dyads real-time visualizations of the extent to which their brainwaves (EEG signals) were "in sync". Our results showed that, compared to a sham control group, dyads who received multi-brain neurofeedback exhibited an increase in inter-brain coupling, and, critically, that this increase was associated with a higher sense of social connectedness. A chain mediation analysis suggested that this experience of enhanced social connectedness may have been driven by a sense of joint control and shared intentionality. Together, our findings showcase the potential for regulating inter-brain coupling to optimize human social relationships and behaviors.

neuroscience↗

bioRxiv2025

CRISPRi-Linked Multi-Module Negative Feedback Loops to Address Winner-Take-All Resource Competition

Cellular resource limitations create unintended interactions among synthetic gene circuit modules, compromising circuit modularity. This challenge is particularly pronounced in circuits with positive feedback, where uneven resource allocation can lead to Winner-Takes-All (WTA) behavior, favoring one module at the expense of others. In this study, we experimentally implemented a Negatively Competitive Regulatory (NCR) controller using CRISPR interference (CRISPRi) and evaluated its effectiveness in mitigating WTA behavior in two gene circuits: dual self-activation and cascading bistable switch. We chromosomally integrated a tunable dCas9 gene and designed module-specific gRNAs, with each module encoding its own gRNA to self-repress via competition for limited dCas9. This configuration introduces strong negative feedback to the more active module while reallocating resources to the less active one, promoting balanced module activation. Compared to the control group lacking dCas9-mediated repression, the NCR controller significantly increased module coactivation and suppressed WTA behavior. Our quantitative results demonstrate that NCR provides an effective strategy for regulating resource competition and improving the modularity of synthetic gene circuits.

synthetic biology↗

bioRxiv2025

High-Throughput Machine Learning-Aided Antibody Discovery for Cell Surface Antigens

Machine learning (ML) has the potential to revolutionize antibody design and selection, but its success depends on access to extensive, well-curated datasets of antibody-antigen interactions. To address this need, we developed a synthetic Fab yeast display library optimized for seamless ML integration, focusing on sequence diversity within the CDRH3 loop. The library incorporates key sequence features derived from human B cell repertoires essential for efficient antibody generation captured in a compact antigen recognition module (ARM) format. Built using the VH1-69 heavy chain and four light chains, the library was evaluated against ten human and murine cell surface antigens, including PD-L1, TIGIT, and ROBO1. This approach yielded hundreds of antibodies with robust biophysical properties, validated for functional performance in flow cytometry and immunohistochemistry. Furthermore, ML analysis identified additional antibodies for ROBO2 and PD-L2 from the aggregate sequencing data, demonstrating utility for hybrid in silico and experimental workflows. We provide a publicly accessible dataset comprising more than 68,000 Fab sequences and 486 characterized antibodies. This study establishes an ML-compatible framework designed to accelerate and streamline antibody discovery and development.

biophysics↗

bioRxiv2025

From cognition to compensation: Neurocomputational mechanisms of guilt-driven and shame-driven altruistic behavior

Guilt and shame are key moral emotions that influence mental health and regulate social behavior. Although prior research has examined the psychological and neural correlates of these emotions, the cognitive antecedents that trigger them, as well as their transformation into social behavior, remain insufficiently understood. In this study, we developed a novel task to investigate how two crucial cognitive antecedents, harm and responsibility, elicit guilt and shame, and how these emotions subsequently drive compensatory behavior, by combining functional magnetic resonance imaging (fMRI) with computational modeling. Behaviorally, we found that harm had a stronger impact on guilt than on shame, whereas responsibility had a stronger impact on shame than guilt, which supports the functionalist theory of emotion. Moreover, compared to shame, guilt exerted a greater effect on compensation. Computational modeling results indicated that the integration of harm and responsibility by individuals is consistent with the phenomenon of responsibility diffusion. The fMRI results revealed that brain regions associated with inequity representation (posterior insula) and value computation (striatum) encode this integrated measure. Furthermore, individual differences in responsibility-driven shame sensitivity were associated with activity in theory-of-mind regions (temporoparietal junction and superior temporal sulcus). Guilt- and shame-driven compensatory behavior recruited distinct neural substrates, with shame-driven compensatory sensitivity being more strongly linked to activity in the lateral prefrontal cortex, a region implicated in cognitive control. Our findings provide computational, algorithmic, and neural accounts of guilt and shame.

neuroscience↗

bioRxiv2025

Integrating Recombinase-Based Feedback and Feedforward Control for Optimal Resource Decoupling

Resource competition disrupts circuit modularity by introducing unintended coupling between otherwise independent gene modules, thereby compromising genetic circuit function. While various control strategies have been explored, their complexity or limited efficacy has hindered broader application. Here, we present the Re-NF-FF-Controller, a recombinase-based strategy that integrates negative feedback and feedforward regulation via promoter flipping to mitigate resource competition. Computational modeling and experimental validation demonstrate that Re-NF-FF-Controller effectively reduces resource coupling, ensuring robust gene expression and modularity. Moreover, its tunability allows for performance optimization through straightforward adjustments of recombinase enzyme levels. This strategy offers a versatile and easily implementable solution for designing reliable synthetic biological systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/653855v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@6b960forg.highwire.dtl.DTLVardef@148bc3borg.highwire.dtl.DTLVardef@3df13borg.highwire.dtl.DTLVardef@a865f2_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Bridging 3D Molecular Structures and Artificial Intelligence by a Conformation Description Language

Artificial intelligence, particularly language models (LMs), is reshaping research paradigms across scientific domains. In the fields of chemistry and pharmacy, chemical language models (CLMs) have achieved remarkable success in two-dimensional (2D) molecular modeling tasks by leveraging one-dimensional (1D) representations of molecules, such as SMILES and SELFIES. However, extending these successes to three-dimensional (3D) molecular modeling remains a significant challenge, largely due to the absence of effective 1D representations for capturing 3D molecular structures. To address this gap, we introduce ConfSeq, a novel molecular conformation description language that integrates SMILES with internal coordinates including dihedral angles, bond angles, and pseudo-chirality. This design naturally ensures SE(3) invariance, while preserving the human readability and conciseness characteristic of SMILES. ConfSeq enables the reformulation of a range of 3D molecular modeling tasks, such as molecular conformation prediction, 3D molecular generation, and 3D molecular representation, into sequence modeling problems. Then, by simply employing a standard Transformer architecture, we achieve state-of-the-art performance on various benchmark sets. Furthermore, compared to widely used diffusion-based approaches in 3D molecular modeling, the ConfSeq-based method offers unique advantages in inference efficiency, generation controllability, and enables scoring of generated molecules. We believe that ConfSeq can serve as a foundational tool, advancing the development of sequence-based 3D molecular modeling methods.

bioinformatics↗

bioRxiv2025

Pln1 Mediates Lipid Droplet-Vacuole Tethering During Microlipophagy Saccharomyces cerevisiae

Lipid droplets (LDs) are dynamic organelles that undergo growth or degradation depending on the metabolic state of the cell. One form of LD degradation is autophagy-mediated, referred to as lipophagy. Here, we demonstrate that Pln1, a perilipin located on the surface of LDs in Saccharomyces cerevisiae, previously known for its role in LD biogenesis, is essential for lipophagy. Pln1 facilitates the docking of cytosolic LDs to vacuoles, the lysosome-like organelles responsible for LD degradation, under various nutrient conditions. Molecular dissection of Pln1 revealed that the N-terminal PAT (Perilipin (PLN1), Adipophilin (PLN2), and TIP47 (PLN3)) domain and a hydrophobic region are critical for the localization and binding of LDs to vacuoles. Site-specific mutagenesis within the PAT domain identified a semi-hydrophobic LD Interacting Motif (LIM), which is vital for this interaction. Furthermore, an intrinsically disordered region (IDR) near the center of Pln1 is required for efficient LD-vacuole tethering. These findings support a model in which Pln1 bridges LDs and vacuoles by simultaneously interacting with both organelles. Notably, deleting PLN1 did not impair survival during prolonged nitrogen starvation and enhanced viability in autophagy-defective (atg8{Delta}) cells, suggesting that balancing Pln1-mediated LD biogenesis and lipophagy is crucial for yeast survival under starvation conditions.

cell biology↗

bioRxiv2025

Targeting Siglec-10/α3β1 Integrin Interactions Enhances Macrophage-Mediated Phagocytosis of Pancreatic Cancer

Tumor-associated macrophages (TAMs) in the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) exhibit immunosuppressive phenotypes and impaired phagocytic activity, facilitating tumor progression and immune evasion. Here, we identify integrin 3{beta}1, composed of ITGA3 and ITGB1 subunits, as a sialylated glycoprotein ligand for Siglec-10, an inhibitory glyco-immune checkpoint receptor highly expressed on TAMs in PDAC. The interaction between Siglec-10 on TAMs and 3{beta}1 on PDAC cells suppresses macrophage-mediated phagocytosis, thereby promoting immune evasion. Consistently, disrupting Siglec-10 interactions with monoclonal antibodies significantly enhances macrophage phagocytosis of PDAC cells and alleviates myeloid cell-mediated inhibition of T cell proliferation and activation in vitro. In both a PDAC xenograft mouse model engrafted with human macrophages and a human Siglec-10 transgenic mouse model, targeting Siglec-10 with monoclonal antibodies reduces PDAC tumor growth. These findings suggest that Siglec-10 interactions are key mediators of TAM-driven immune evasion in PDAC and highlight the therapeutic potential of targeting these interactions to restore anti-tumor immunity. SIGNIFICANCEPancreatic tumor cells exploit integrin 3{beta}1 to engage the immunosuppressive checkpoint receptor Siglec-10 on myeloid cells, driving immune evasion, and antibody-mediated blockade of Siglec-10 restores myeloid cell-mediated anti-PDAC immunity.

immunology↗

bioRxiv2025

ZapC crosslinks FtsZ filaments through a dual-binding mechanism modulated by the intrinsically disordered linker of FtsZ

Most bacteria divide through binary fission, which is mediated by a large protein complex called the divisome. Assembly of the divisome is initiated by formation a Z ring at midcell consisting of polymers of the bacterial tubulin FtsZ. A series of FtsZ-associated proteins (Zaps), which crosslink FtsZ filaments, promote Z ring formation in Escherichia coli. However, how these proteins interact with FtsZ is still unclear. In this study, we discover that ZapC binds to both FtsZs globular domain and its conserved C-terminal peptide (CCTP) to crosslink FtsZ filaments. An AlphaFold 3 structural model of the FtsZ-ZapC complex indicates that ZapC binds to the globular domain of FtsZ via a loop region connecting its N-terminal and C-terminal domains and to the CCTP of FtsZ via a hydrophobic pocket in the N-terminal domain. Substitutions in these regions of ZapC disrupt its binding to FtsZ, validating the dual binding mode. Strikingly, we find that the intrinsically disordered C-terminal linker (CTL) of FtsZ affects the interaction of FtsZ with ZapC as well as other partners, indicating an important role of the CTL in FtsZ functionality. Taken together, these results indicate that ZapC, although it exists as a monomer, can crosslink FtsZ filaments by a two-pronged mechanism, binding to the globular domain of FtsZ in one filament and to the CCTP of FtsZ in another filament. Furthermore, the CTL plays an important role in regulating FtsZ interaction with its partners. ImportanceBacterial cytokinesis requires the Z ring, a highly dynamic cytoskeletal element consisting of polymers of the bacterial tubulin FtsZ. Formation of a coherent and functional Z ring is facilitated by FtsZ-associated proteins (Zap), which can crosslink FtsZ polymers, but how these proteins work is still incompletely understood. In this study, we find that ZapC, one of the FtsZ crosslinkers, binds to both FtsZs globular domain and its conserved C-terminal peptide to crosslink FtsZ filaments. Moreover, the intrinsically disordered C-terminal linker (CTL) of FtsZ modulates its binding to ZapC and many other FtsZ binding proteins. These findings reveal a novel mechanism to crosslink FtsZ filaments and reveal an important and highly conserved role of the CTL in FtsZ functionality.

microbiology↗

bioRxiv2025

GenVS TBDB: An Open AI-Generated andVirtual Screened Small-Molecule Database for Tuberculosis Drug Discovery

Tuberculosis (TB) remains a leading global health threat, with over 10 million new cases and 1.25 million deaths reported in 2023. Current TB therapies rely on a limited drug repertoire and prolonged treatment courses that have changed little in four decades. Here, we present GenVS-TBDB, a target-aware AI-generated and virtual-screened small-molecule database, which expands the chemical space against Mycobacterium tuberculosis (M.tb) essential proteins. We first identified 460 probable small-molecule binding pockets across 377 essential M.tb proteins by integrating multiple sources. Then, by leveraging the target-aware molecule generative model, over 1.2 million novel small molecules tailored to these pockets were produced. The key physicochemical properties were computed for all compounds to ensure medicinal chemistry tractability. These compounds were also evaluated using molecular docking and anti-TB specific graph neural network model, yielding binding propensity ranking and whole-cell activity prioritization for each target. To substantiate the integrated AI-driven workflow for anti-TB discovery, 30 compounds were obtained, including 22 AI-designed molecules synthesized de novo and 8 commercially available analogs. In validation, 2 synthesized compounds demonstrated significant thermal stabilization of FtsZ, confirming target engagement. 6 compounds exhibited cellular inhibition below 50 {micro}M, the most potent at 12 {micro}M. Furthermore, GDI-11785 showed binding to the cell wall biosynthesis pathway with 35 {micro}M cellular activity, establishing a promising starting point for tuberculosis drug discovery. Our findings contribute a significant library of bioactive molecules which may hasten the preliminary phase of tuberculosis drug discovery. The GenVS-TBDB small library is publicly accessible and can be downloaded freely at https://datascience.ghddi.org/database/view.

pharmacology and toxicology↗

bioRxiv2025

Horizontal transfer of a 180-kbp genomic fraction among the largest viral genomes

Viruses are generally considered tiny biological entities with small genomes; however, some dsDNA viruses, known as giant viruses, have large genomes that are comparable to those of small bacteria. Previous studies indicated that the genomes of giant viruses expanded from a small ancestor by a combination of gene duplication, de novo gene creation, and horizontal gene transfer (HGT). Among them, virus-to-virus HGTs are recently recognized as an important mechanism for disseminating functional genes between giant viruses. In this study, we isolated a giant virus of a member of pandoraviruses, which have the largest genome sizes reaching 2.5 Mbp. Based on the average nucleotide identity of known pandoraviruses, this new pandoravirus belongs to an existing viral species. However, its genome was approximately 200 kbp larger than those of the other strains from the same species. A genome-wide comparison identified a 180-kbp region with 168 genes missing from the other strains but found in phylogenetically distant pandoraviruses. The GC ratio and homology of the deduced amino acid sequences in this 180-kbp region suggest that the new virus horizontally acquired this region from a distantly related pandoravirus. The gene composition in the 180-kbp region further indicates that this region was already large at the time of the horizontal transfer. Our findings suggest that pandoraviruses can horizontally exchange a large portion of their genomes. This event presumably represents one mechanism for accelerating genomic evolution and gigantism in giant viruses.

microbiology↗