Biology subjects

Liu, K.

Publications and source records attributed to Liu, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Optical Windows for Transcranial Brain Imaging in Living Mice: Skull Thinning, Clearing, and Beyond

Longitudinal, noninvasive in vivo imaging is essential for studying brain physiology and pathological mechanisms. Advances in transcranial optical windows, including thinned-skull and optical clearing techniques, have markedly improved imaging depth and resolution when combined with multiphoton microscopy. However, their optical performance often deteriorates rapidly, and quantitative studies on long-term stability and the causes of image quality loss remain limited. In this work, we systematically investigated current transcranial window approaches using multiphoton excited fluorescence microscopy (MPEFM) and adaptive optics, examining longevity, optical aberrations, and imaging resolution. Our results reveal that progressive skull regrowth is a fundamental limitation across all window types, leading to substantial declines in signal quality and resolution for conventional MPEFM thereby reducing achievable high-resolution imaging depth. To address these challenges, we developed a localized glucocorticoid (GC) delivery strategy that significantly extends window performance for up to one month. Furthermore, we demonstrated that a GC-loaded hydrogel sealing method effectively suppressed skull regrowth while preserving optimal optical properties, offering a potential and practical route to chronic, high-fidelity transcranial imaging. These findings provide mechanistic insight into window degradation and establish a framework for sustained, long-term in vivo brain imaging.

neuroscience↗

bioRxiv2026

Connectome lateralization in autism across the first 14 years: heterogeneity related to developmental stage, hemisphere, and pathophysiology

Hemispheric lateralization is fundamental feature to neurodevelopment, yet its dynamic evolution in autism across childhood and underlying molecular mechanisms remain unknown. Thus, using a large-scale resting-state fMRI dataset (n = 1553, ages 1-14), we investigated developmental heterogeneity in connectome lateralization. At the group level, abnormalities in dynamic connectome lateralization strength (DCLS) progressed from focal patterns in early childhood ([≤] 6 years) to widespread distributions by late childhood ([≤] 14 years), independent of symptom severity. The late-stage patterns were validated using the ABIDE dataset (n=153). Late childhood also showed marked increases in inter-individual heterogeneity. These alterations were significantly associated with clinical phenotypes, transcriptomic profiles, and multiple neurotransmitter systems, with distinct patterns across childhood groups. Our findings reveal a developmentally dynamic trajectory of connectome lateralization in autism and highlight late childhood as a critical window for stage- and individual-specific interventions tailored to substantial individual heterogeneity.

neuroscience↗

bioRxiv2026

Stool Metabolomics Reveals Catecholamine and Tryptophan-NAD+ Pathway Alterations in Autism Spectrum Disorder

Gut-brain axis dysregulation and microbiome-linked metabolic disturbances have been implicated in autism spectrum disorder (ASD), yet gut-derived neuroactive metabolites remain incompletely characterized. We applied targeted liquid chromatography-tandem mass spectrometry in a cross-sectional case-control study to quantify 18 stool metabolites related to catecholamine synthesis, GABAergic signaling, and tryptophan (Trp) and NAD+ metabolism in 59 participants (32 ASD, 27 non-ASD controls). Group differences were evaluated using log2 fold change and covariate-adjusted linear models. Random forest classifiers with five-fold cross-validation assessed multivariate discriminative performance, and within-group Spearman correlations examined metabolic network organization. Norepinephrine exhibited the largest elevation in ASD, while dopamine and tetrahydrobiopterin showed nominal group effects consistent with altered BH4-dependent catecholamine metabolism. Among individual metabolites, tetrahydrobiopterin, GABA, and kynurenine were the most informative, and their combination achieved an area under the receiver operating characteristic curve of 0.737 (95% confidence interval, 0.603 to 0.871). Correlation analyses revealed conserved lithocholic acid-deoxycholic acid coupling in both groups. In controls, Trp correlated with kynurenine, whereas ASD showed expanded Trp associations with GABA, norepinephrine, anandamide, and nicotinic acid, consistent with reorganization of Trp-NAD+ precursor pathways. These findings identify coordinated, gut-linked metabolic differences in ASD and define a metabolite signature reflecting altered catecholaminergic and Trp-related network structure. ImportanceAutism spectrum disorder is currently diagnosed using behavioral assessments, and objective biological measures are limited. The gut microbiome produces many small molecules that can influence brain development and function, but the specific metabolites involved in ASD remain unclear. Using targeted analysis of stool samples, we identified changes in metabolites related to neurotransmitter synthesis and tryptophan metabolism and showed that their relationships form distinct metabolic networks in individuals with ASD. A small panel of metabolites provided moderate ability to distinguish ASD from controls. These results suggest that gut-derived metabolites capture biologically meaningful variation in ASD and may help guide future studies aimed at understanding gut-brain communication and developing noninvasive biomarkers.

microbiology↗

bioRxiv2026

Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction

Mass spectral libraries have become essential resources for training deep learning (DL) models for spectral prediction and de novo sequencing in bottom-up mass spectrometry (BU-MS). Compared with BU-MS, top-down MS (TD-MS) offers unique advantages for characterizing intact proteoforms by analyzing proteoforms without enzymatic digestion. Despite these advantages, large-scale spectral libraries for TD-MS are currently lacking. Here we present TopRepo, the first comprehensive and publicly available repository of TD-MS spectra, comprising more than 12 million spectra acquired from 12 species across seven types of mass spectrometers. Using TopRepo, we constructed a large-scale top-down spectral library containing over 5 million spectra with proteoform and fragment-ion annotations. We demonstrate that TopRepo enables pan-dataset analyses of N-terminal processing, mass shifts, and other proteoform characteristics identified by TD-MS. Furthermore, we show that the TopRepo spectral library substantially improves proteoform identification through spectral library searching and supports the training of DL models for high-accuracy top-down spectral prediction.

bioinformatics↗

bioRxiv2026

Distinct and cooperative roles of host and tumor Osteopontin in colorectal cancer liver metastasis

Osteopontin (OPN) is a secreted phosphoprotein implicated in colorectal cancer liver metastasis (CRCLM), yet the distinct spatial contributions of host-and tumor-derived OPN in driving this disease remain unclear. Using a 2 x 2 genetic knockout mouse model targeting OPN in host and tumor compartments, combined with spatial transcriptomics, we investigated compartment-specific OPN functions in CRCLM. Tumor-derived OPN promotes tumor proliferation through MEK/ERK signaling. Host OPN licenses monocyte-to-macrophage differentiation, while tumor OPN polarizes macrophages towards an M2-like state. Both host and tumor OPN suppress T cells in the tumor microenvironment, whereas loss of host OPN reveals an interferon-driven, anti-tumor niche. Translational studies using OPN-blockade immunotherapy in syngeneic and patient-derived xenograft mouse models reduced tumor burden and enhanced T cell infiltration. Together, these findings redefine the OPN-myeloid paradigm in CRC and nominate OPN as a potential therapeutic target.

immunology↗

bioRxiv2026

Autoregressive forecasting of future single-cell state transitions

Predicting future cell state transitions from static transcriptomic snapshots is vital for understanding and steering cellular dynamics. Although existing trajectory and RNA velocity methods can infer local transitions within observed data, they are fundamentally limited in extrapolating long-range cellular dynamics. Here, we introduce CellTempo, an autoregressive generative framework that enables long-range forecasting of cell state trajectories directly from static transcriptomic snapshots. CellTempo is pretrained on scBaseTraj, a large-scale collection of multi-step cellular transition sequences constructed by integrating diverse experimental technologies and data sources. Across diverse biological systems, CellTempo accurately predicts long-range lineage progression and reconstructs unseen cellular potential landscapes. It further distinguishes transient perturbation responses from long-term cell-fate changes, enabling prioritization of candidate compounds for cell-fate engineering. These results demonstrate that long-range cellular dynamics are inferable from static observations, establishing a foundation for predictive and controllable modeling of cell fate.

bioinformatics↗

bioRxiv2026

AI-driven discovery and engineering of human endogenous nanocage proteins for mRNA delivery

Safe and effective gene delivery remains a central challenge for therapeutic applications. While non-viral and viral vectors have enabled substantial progress, their reliance on non-human components often triggers immune responses, limiting their use in chronic treatments. Here, we developed DeepDelivery, an artificial intelligence-driven platform to repurpose human proteins for mRNA delivery. An unbiased screening of the human proteome nominated 512 candidates, with experimental validation confirming that 80% of top-ranked hits form mRNA-encapsulating particles and mediate efficient functional delivery in human cells without provoking detectable inflammation. Notably, multiple tripartite motif (TRIM) family proteins, typically linked to antiviral responses, exhibited strong assembly and delivery activity. Quantitative analysis and interpretation of the model revealed structural domains that govern nanocage formation, enabling domain-guided engineering of TRIM25 variants with enhanced function. Our work establishes a generalizable framework for discovering human-derived delivery vehicles and provides a path toward programmable, non-immunogenic mRNA therapeutics.

synthetic biology↗

bioRxiv2026

Reversible RNA Acylating Reagents with Nitro Reduction Strategy

We developed a series of nitro reduction-reversible acylating reagents. Following optimization of the acylation conditions, these reagents were tested for deacylation with sodium dithionite in vitro. We applied this reversible acylation to modulate RNAzyme-mediated pre-tRNA maturation, demonstrating its ability to regulate RNA-RNA interactions. Furthermore, the in vitro reversible acylation of EGFP mRNA indicated effective control of its translational activity. To explore cellular applications, we validated NQO1-mediated deacylation in vitro and then induced hypoxia in HepG2 cells using cobalt chloride, thereby reactivating the function of acylated EGFP mRNA via endogenous NQO1. Overall, this study highlights the potential for developing nitro reduction-reversible acylation as a new strategy for RNA functional control and RNA-based drug modification.

biochemistry↗

bioRxiv2026

Calcium directs actin assembly via allosteric activation of formin INF2

Calcium signals spatiotemporally orchestrate cytoskeletal dynamics, typically through Rho GTPase-mediated signaling cascades, yet the direct molecular transducers that convert local calcium transients into spatially controlled actin assembly have remained elusive. Here, we uncover a structure-based mechanism by which calcium-bound calmodulin (Ca2+-CaM) directly activates formin INF2 to drive actin assembly. We demonstrate that Ca2+-CaM binds to the diaphanous inhibitory domain (DID) of INF2 with nanomolar affinity, inducing allosteric conformational changes that sterically disrupt INF2 autoinhibition. The unexpected bipartite Ca2+-CaM binding interface on INF2 enables ultrasensitive decoding of local calcium microdomains, such as ER-mitochondrial contacts, where activated INF2 promotes actin polymerization to facilitate mitochondrial fission. We further show that the Charcot-Marie-Tooth disease-associated INF2 R91G mutation enhances Ca2+-CaM binding via optimized interfacial dynamics, suggesting a gain-of-function disease mechanism. Our work establishes the Ca2+-CaM-INF2 axis as a direct molecular transducer linking spatial calcium signals to actin-dependent organelle dynamics, defining a Rho-GTPase-independent paradigm for calcium-cytoskeleton communication, with broad implications for INF2-linked pathologies.

biochemistry↗

bioRxiv2026

Single-nuclei RNA-sequencing uncovers sexually divergent exercise signatures partially mimicked by TFEB overexpression in mouse skeletal muscle

Exercise induces extensive, cell-type-specific transcriptional remodeling in skeletal muscle to support metabolic flexibility and adaptation. However, the regulatory mechanisms underlying these transcriptional programs, and the extent to which they differ between sexes, remain poorly defined. We previously reported that lifelong, muscle-specific overexpression of human Transcription Factor E-B (cTFEB;HSACre transgenic mice) recapitulates many adaptive features of endurance training in both sexes, leading to profound geroprotective effects during aging even in the absence of exercise. Here, we profile transcriptional adaptations to voluntary wheel running (VWR) and TFEB-overexpression at single-nucleus resolution in young male and female mouse tibialis anterior muscle. This represents, to our knowledge, the first integrated analysis of exercise and TFEB signaling using sex as a biological variable. Using robust bioinformatic and single-nuclei RNA-sequencing approaches, we profiled six muscle-resident cell populations and uncover previously unrecognized, sex-dependent signaling nodes governing exercise-associated metabolic plasticity. TFEB activation and endurance training by VWR elicit strongly correlated transcriptional programs enriched for lipid metabolism, mitochondrial remodeling, and immune modulation, establishing TFEB-overexpression as a partial exercise mimetic. In general, female muscle exhibited enhanced extracellular matrix and lipid-associated responses to endurance training and TFEB overexpression, whereas males preferentially engaged in angiogenic and oxidative networks, revealing distinct sex-specific, sex-dimorphic, or sex-agnostic regulatory routes to metabolic flexibility. Integration with independent multi-omics datasets from endurance-trained rats (MoTrPAC) confirms the conservation of TFEB-exercise transcriptional convergence in skeletal muscle across species and potentially muscle types. Together, these findings define TFEB as a regulator of exercise transcriptional programs and reveal sex-specific molecular frameworks that drive metabolic adaptation in skeletal muscle. Furthermore, the resulting sex-resolved, single-nucleus transcriptional atlas provides a unique resource for the field, enabling comparative, mechanistic, and hypothesis-driven exploration of exercise-responsive skeletal muscle regulatory networks across sexes.

physiology↗

bioRxiv2026

Asymmetric partition of the O-GlcNAcome in mitosis ensures binary cell fate decision

Many cellular components undergo biased segregation during stem cell division, but whether such order extends to the proteome has remained unknown. Using our real-time O-GlycoTracer, we find that O-GlcNAcylated proteins (the O-GlcNAcome) segregate asymmetrically during Drosophila neuroblast mitosis, predisposing the two daughters to distinct fates. The daughter that preserves stem cell identity inherits most of the O-GlcNAcome. This asymmetric partition requires putative O-GlcNAc readers, notably 14-3-3 proteins. We further identify the nuclear pore complex (NPC) as a major O-GlcNAc substrate in neuroblasts; Nup153, located in the nuclear basket, shows O-GlcNAc-dependent biased inheritance. Perturbing multiple steps in this segregation pathway disrupts neuroblast differentiation, reduces brain size, and causes adult learning deficits. These findings reveal a coordinated O-GlcNAc-driven mechanism for proteome-level asymmetric inheritance during neural stem cell division, with implications for neurodevelopmental disorders linked to OGT or 14-3-3 mutations.

cell biology↗

bioRxiv2025

Tibetan near-complete pangenome reveals complex variants underlying high-altitude adaptation

Genomic diversity in indigenous populations offers critical insights into human evolution and population-specific adaptation. Here, we generated 70 near-complete, fully phased genome assemblies from 35 high-altitude Tibetan trios and identified 4.55 million small variants and 63,031 structural variants (SVs) absent from the current global pangenome reference. Comparative analyses with a 595 globally diverse long-read genome dataset revealed 207 previously uncharacterized Tibetan-enriched SVs spanning 275 genes implicated in high-altitude physiological adaptation. Genotyping these SVs in 1,164 Tibetan and Han individuals with 88 physiological traits reveals five variants significantly associated with cardiopulmonary and hematological phenotypes central to hypoxia adaptation. We further map 2.45 Gb of archaic hominin sequences in Tibetans and uncover 18 previously unrecognized introgressed regions enriched in Tibetans with genes related to hematopoiesis and lung function. These regions harbor five Tibetan-enriched SVs, indicating that archaic introgression contributed SVs relevant to human adaptation. Together, these findings reveal substantial uncharacterized genomic diversity in Tibetans and highlight a previously underappreciated role of SVs and archaic SVs in shaping human evolution and high-altitude adaptation.

genomics↗

bioRxiv2025

A near-complete lamprey genome illuminates ancestral vertebrate innovations

The origin of vertebrates is characterized by a suite of phenotypic innovations, yet the underlying genetic mechanisms remain poorly understood. As a living representative of jawless vertebrates, the lamprey serves as a pivotal model for investigating the genomic basis of early vertebrate evolutioin. Here, we report a near telomere-to-telomere (T2T) genome assembly of the reissner lamprey (Lethenteron reissneri), generated from sperm DNA that is not subject to programmed genome rearrangement. The 1.25 Gb assembly resolves over 97% of chromosome sequences into single contigs, enabling reconstruction of previously inaccessible genomic regions. Centromeres display highly diversified, lamprey-specific repeat units and structural architectures, whereas telomeres contain both conserved and lineage-specific satellite repeats. Deep transcriptomic profiling across representative organs and developmental stages substantially improved genome annotation. Comparative genomic analyses revealed a major expansion of 1,562 gene families at the base of the vertebrate lineage, and they are significantly enriched for functions related to neural development, skeletal formation, and cardiac function, echoing the known phenotypic innovations in vertebrates. Notably, the CDH2 gene family underwent vertebrate-specific copy number expansion and acquired conserved cis-regulatory elements (CREs), highlighting its potential role in shaping the early vertebrate circulatory system. Histological analyses and functional knockout experiments demonstrated that one CDH2 paralog (CDH2_H) is essential for lamprey heart development and chamber formation, playing a critical role in the emergence of the closed circulatory system in early vertebrates. This high-quality lamprey genome provides a foundational resource for dissecting the genetic basis of key innovations that shaped vertebrate evolution.

genomics↗

bioRxiv2025

A high-throughput methods SNIPR-Nm reveals small RNA methylation ratio

Small RNAs regulate gene expression and genome stability, and their functions are shaped by 3'-terminal 2'-O-methylation (Nm). Although Nm is universal in plants and mainly marks animal piRNAs, recent evidence reveals Nm on mammalian miRNAs, highlighting broader regulatory roles. However, current sequencing underestimates Nm-modified RNAs due to ligation bias, and existing qPCR-based methods cannot simultaneously quantify abundance and modification, leaving Nm dynamics largely unexplored. We developed a unified enzymatic strategy that integrates poly(A) polymerase and a thermostable ligase to measure both small RNA abundance and 3'-end Nm status. Applied to mouse testis, it enables robust quantification of Nm ratios for piRNAs and miRNAs. Our method offers a versatile tool for dissecting small RNA methylation in development and disease.

genetics↗

bioRxiv2025

Emergence of hypervirulent Klebsiella pneumoniae ST111 with a novel virulence plasmid causing pyogenic liver abscess

Hypervirulent Klebsiella pneumoniae (hvKp)-associated pyogenic liver abscess is typically linked to K1/K2 capsule serotypes and canonical lineages such as ST23, ST65, and ST86. Cases outside these lineages are rare but pose significant public health concerns. We investigated an unusual liver abscess in an immunocompetent patient caused by hvKp sequence type 111 (ST111). Five isolates (KP1-KP5) were recovered, all belonging to the same clonal lineage. Genomic analysis revealed a 181 kb IncHI1B/IncFIB virulence plasmid encoding rmpADC and the salmochelin cluster (iroBCDN), but lacking aerobactin (iuc) and rmpA2 gene loci. Notably, this plasmid also carried the yersiniabactin locus (ybt), which is typically located on the chromosome. Comparative genomics indicated that similar ST111 strains have been reported only in China, suggesting clonal expansion of a previously unrecognized hvKp lineage. Functional assays demonstrated that plasmid curing abolished the hypermucoviscous phenotype, reduced capsule production, and completely attenuated virulence in murine models, confirming the plasmid as the major driver of hypervirulence. Interestingly, plasmid loss enhanced biofilm formation and relieved growth burden, highlighting fitness trade-offs associated with virulence. This study documents a rare case of hvKp ST111 liver abscess and identifies a novel plasmid conferring hypervirulence. Our findings expand the known diversity of hvKp and underscore that non-canonical lineages can acquire potent virulence determinants enabling severe disease. Continued clinical and genomic surveillance is essential to detect emerging hvKp clones before widespread dissemination.

microbiology↗

bioRxiv2025

Structure-informed evolutionary analysis of the meiotic recombination machinery

Despite being essential for fertility, many proteins involved in meiotic homologous recombination have diverged rapidly. The evolutionary forces driving this divergence remain mostly unknown, in part because of challenges in accounting for the interplay of sequence changes with constraints imposed by proteins structures and physiological roles. Here, we explore strategies to more sensitively detect signatures of positive or relaxed selection by integrating evolutionary analyses with structural and functional information, using meiotic recombination proteins in four taxa--primates, rodents, birds and budding yeasts. By mapping selection rate estimates onto predicted protein structures, we characterized protein regions likely to have experienced positive selection. We further identified subtle sequence variation within protein domains that are well conserved generally because of structural constraints. To detect sequence variation masked by these constraints, we analyzed selection at structurally matched residues, comparing homologs across different lineages as well as between meiosis-specific and generalist paralogs. These approaches identified lineage- and paralog-restricted enrichment of non-synonymous substitutions that may indicate loss of functional constraints and/or adaptive innovation. Finally, we used cross-species complementation experiments in Saccharomyces cerevisiae to show that sequence variation in the pro-crossover factor MSH4 modulates recombination proficiency. We suggest that evolutionary plasticity per se is a key conserved characteristic of the meiotic recombination machinery. More generally, our approach provides a mechanistic framework to analyze protein evolution.

evolutionary biology↗

bioRxiv2025

pGGTOX: a versatile plasmid platform for recombination-based genome editing across Enterobacteriaceae

Precise genome editing in Enterobacteriaceae is essential for studying gene function, pathogenesis, and antimicrobial resistance, yet many current systems face host-specific and efficiency limitations. We developed pGGTOX, a modular plasmid platform that enables efficient homologous recombination-mediated genome editing across diverse Enterobacteriaceae, including Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, and Enterobacter intestinihominis. The system integrates a rhamnose-inducible toxin (MqsR) for stringent counterselection, a sfGFP reporter for visual tracking of recombination events, Golden Gate cloning for rapid assembly of homologous arms, an FRT-flanked resistance cassette for marker removal, and an oriT sequence for conjugative transfer. Together with the companion plasmid pCP20-oriT, pGGTOX supports precise, marker-free genomic modification. Using pGGTOX, we achieved targeted deletions of dapA in E. coli and mrkCD in carbapenem-resistant K. pneumoniae, both with 100% efficiency. The dapA mutant exhibited diaminopimelate auxotrophy, while mrkCD deletion markedly reduced biofilm formation, consistent with the loss of function associated with these genes. pGGTOX also enabled deletion of a 43.1-kb type IV secretion gene cluster (tra) from an IncN/FII plasmid in E. intestinihominis and insertion of a 10-kb CRISPR-Cas9 plasmid-curing module (pCasCure) into an S. enterica IncX1 plasmid. Deletion of the tra gene cluster resulted in a substantial reduction in plasmid conjugation efficiency. Conjugative transfer of the engineered IncX1-pCasCure plasmid into K. pneumoniae facilitated CRISPR-mediated curing of blaKPC, sensitizing carbapenem resistance to susceptibility. In summary, pGGTOX provides a versatile, efficient, and broadly applicable platform for genome engineering and CRISPR delivery in Enterobacteriaceae, expanding the toolkit for bacterial genetics and translational antimicrobial research. ImportancePrecise genetic manipulation in Enterobacteriaceae remains a major technical challenge, particularly for non-model or multidrug-resistant strains. We developed pGGTOX, a versatile and broadly applicable plasmid platform that enables efficient, marker-free genome editing through homologous recombination. By integrating stringent counterselection, visual screening, modular cloning, and conjugative transfer, pGGTOX simplifies construction and streamlines editing across multiple clinically relevant species. We demonstrate its utility in deleting chromosomal and plasmid-borne loci, inserting large genetic modules, and delivering CRISPR-Cas9 systems for targeted elimination of antibiotic resistance genes. This platform expands the molecular toolkit for functional genomics and provides a powerful new strategy for dissecting bacterial virulence, resistance, and plasmid biology.

microbiology↗

bioRxiv2025

Distinct and Shared Impacts of Virulence Plasmids on the Phenotype and Transcriptome in Convergent Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae

The global rise of convergent carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKp) represents a major clinical challenge, yet the role of virulence plasmids (pVirs) in shaping bacterial physiology and pathogenicity remains incompletely understood. Using a CRISPR-Cas9-based curing system, we precisely eliminated pVirs from two clinical CR-hvKp strains with distinct genetic backgrounds, ST23-KL1 (blaNDM-1) and ST11-KL64 (blaKPC-2). Loss of pVir conferred fitness advantages in vitro, reduced capsule production and hypermucoviscosity, and promoted biofilm formation, while markedly attenuating virulence in murine sepsis models. Despite this reduction, the pVir-cured ST23-KL1 strain retained higher virulence than the pVir-cured ST11-KL64 strain, underscoring the contribution of chromosomal background to pathogenic potential. Transcriptomic profiling revealed both shared and strain-specific transcriptional responses to pVir deletion, with broader perturbations observed in the ST11-KL64 strain. pVir removal had limited effects on antibiotic MICs. Complementation experiments further demonstrated differential regulatory roles of the rmpADC and rmpA2D2 operons in capsule expression and hypermucoviscosity across the two strains. Together, these findings establish pVirs as central determinants of CR-hvKp virulence and highlight complex host-plasmid interactions that influence bacterial adaptation and pathogenicity. IMPORTANCEThe emergence of carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKp) poses a critical threat to global health, yet the contribution of virulence plasmids (pVirs) to bacterial fitness and pathogenicity remains poorly defined. By employing a CRISPR-Cas9-based curing strategy, we dissected the role of pVirs in two genetically distinct CR-hvKp strains and uncovered their multifaceted impact on capsule production, hypermucoviscosity, biofilm formation, and virulence. Our findings reveal that pVir loss confers fitness advantages in vitro while attenuating virulence in vivo, with strain-specific transcriptional responses and differential regulation by rmp operons. These results underscore the complex interplay between plasmid-encoded and chromosomal determinants in shaping CR-hvKp pathogenicity and adaptation, offering mechanistic insights that may inform future therapeutic strategies targeting plasmid-mediated virulence.

microbiology↗