Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 361 records · Page 20Linked to original sources

bioRxiv2025

Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in human immune disorders

Adaptive immunity, mediated by T and B cell responses, is essential for defending against infections and cancers while also being implicated in autoimmune diseases. Tracking T and B cell repertoires in situ at single-cell resolution is essential for understanding adaptive immune responses. To address the lack of tools for in situ single-cell T/BCR (XCR) sequencing, we developed Stereo-XCR-seq, an efficient strategy for retrieving and sequencing TCR and BCR from Stereo-seq cDNA libraries at subcellular resolution. Stereo-XCR-seq provides unbiased full-length XCR reads alongside spatial transcriptomics, enabling the identification of heterogeneous lymphoid aggregates with distinct clonal activities in cancers and inflammatory bowel disease (IBD). We identified plasma cell aggregates that differ from tertiary lymphoid structures (TLSs) in both transcriptomic profiles and clonal activities, with spatial positioning potentially mediating unique immune responses. Collectively, Stereo-XCR-seq enables in situ single-cell profiling of T and B cell clonal activities within tissue microenvironments, providing insights into lymphocyte adaption to environmental stimuli. This technology provides potential for advancing our understanding of tissue immunity and the development of therapeutic strategies for immune disorders.

immunology↗

bioRxiv2025

Age-Associated Decline in Autophagy Pathways in Retinal Pigment Epithelium and Protective Effects of Topical Trehalose in Light-induced Outer Retinal Degeneration in Mice

Age is a primary risk factor for chronic conditions, including age-related macular degeneration (AMD). Impairments in autophagy processes are implicated in AMD progression, but the extent of autophagys contribution and its therapeutic potential remain ambiguous. This study investigated age-associated transcriptomic changes in autophagy pathways in the retinal pigment epithelium (RPE) and evaluated the protective effects of topical trehalose, an autophagy-enhancing small molecule, against light-induced outer retinal degeneration in mice. Transcriptomic analysis of human RPE/choroid and mouse RPE revealed consistent downregulation of autophagy pathways with age, alongside variable changes as AMD severity progressed. Given the age- and AMD-associated perturbation of autophagy pathways, we examined trehalose treatment in vitro, which enhanced autophagic flux and restored mitochondrial respiratory function in primary murine RPE cells exposed to oxidative stress. In vivo, topical trehalose improved autophagy-lysosome activity in mouse RPE, demonstrated by elevated LC3B turnover and SQSTM1/p62 degradation. Furthermore, trehalose eyedrops protected mice from light-induced damage to the RPE and photoreceptors, preserving outer nuclear layer thickness, RPE morphology, and junctional F-actin organization. Taken together, the data support that age-related decline and severe dysregulation in autophagy contributed to AMD progression. By restoring autophagic flux, topical trehalose demonstrates therapeutic potential to address early autophagy-related pathological changes in AMD.

pathology↗

bioRxiv2025

Systematic Determination of the Impact of Structural Edits on Accumulation into Mycobacteria

Understanding the factors that influence the accumulation of molecules beyond the mycomembrane of Mycobacterium tuberculosis (Mtb) - the main barrier to accumulation - is essential for developing effective antimycobacterial agents. In this study, we investigated two design principles commonly observed in natural products and mammalian cell-permeable peptides: backbone N-alkylation and macrocyclization. To assess how these structural edits impact molecule accumulation beyond the mycomembrane, we utilized our recently developed Peptidoglycan Accessibility Click-Mediated Assessment (PAC-MAN) assay for live-cell analysis. Our findings provide the first empirical evidence that peptide macrocyclization generally enhances accumulation in mycobacteria, while N-alkylation influences accumulation in a context-dependent manner. We examined these design principles in the context of two peptide antibiotics, tridecaptin A1 and griselimycin, which revealed the roles of N-alkylation and macrocyclization in improving both accumulation and antimicrobial activity against mycobacteria in specific contexts. Together, we present a working model for strategic structural modifications aimed at enhancing the accumulation of molecules past the mycomembrane. More broadly, our results also challenge the prevailing belief in the field that large and hydrophilic molecules, such as peptides, cannot readily traverse the mycomembrane.

microbiology↗

bioRxiv2025

Stress-activated neuronal ensemble in the supramammillary nucleus stores anxiety but not memory

Anxiety is a prevalent negative emotional state induced by stress; however, the neural mechanism underlying anxiety is still largely unknown. We used acute and chronic stress to induce anxiety and test anxiety-like behavior; immunostaining, multichannel extracellular electrophysiological recording and Ca2+ imaging to evaluate neuronal activity; and virus-based neuronal tracing to label circuits and manipulate circuitry activity. Here, we identified a hypothalamic region, the supramammillary nucleus (SuM), plays important role in anxiety-like behavior. We then characterized a small ensemble of stress-activated neurons (SANs) that are recruited by stress. These SANs respond specifically to stress, and their activation robustly increases anxiety-like behavior in male mice. We also found that ventral subiculum (vSub)-SuM projection but not dorsal subiculum (dSub)-SuM projections encode anxiety-like behavior and that inhibition of these vSub-SuM projections has an antianxiety effect. These results indicate that the reactivation of stress-activated supramammillary cells and relevant neural circuits are important neural processes underlying anxiety-like behavior.

neuroscience↗

bioRxiv2025

Chemoproteomic Profiling of C. albicans for Characterization of Anti-fungal Kinase Inhibitors

Candida albicans is a growing health concern as the leading causal agent of systemic candidiasis, a life-threatening fungal infection with a mortality rate of [~]40% despite best available therapy. Yck2, a fungal casein kinase 1 (CK1) family member, is the cellular target of inhibitors YK-I-02 (YK) and MN-I-157 (MN). Here, multiplexed inhibitor beads paired with mass spectrometry (MIB/MS) employing ATP-competitive kinase inhibitors were used to define the selectivity of these Yck2 inhibitors across the global C. albicans proteome. The MIB matrix captured 89% of the known and predicted C. albicans protein kinases present in cell lysate. In MIB/MS competition assays, YK and MN demonstrated exquisite selectivity across the C. albicans fungal kinome with target engagement of only three CK1 homologs (Yck2, Yck22, and Hrr25) and a homolog of human p38 (Hog1). Additional chemoproteomics using a custom MN-kinobead identified only one additional C. albicans protein, confirming its remarkable fungal proteome-wide selectivity. To identify new Yck2 inhibitors with selectivity over Hog1, thirteen human CK1 kinase inhibitors were profiled for fungal kinase-binding activity using MIB/MS competition assays and in-cell NanoBRET target engagement assays. A new chemotype of family-selective Yck2 inhibitors with antifungal activity was identified. Together, these findings expand the application of MIB/MS proteomic profiling for non-human kinomes and demonstrate its utility in the discovery and development of selective inhibitors of fungal kinases with potential antimicrobial activity. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/632200v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1606f86org.highwire.dtl.DTLVardef@39c92borg.highwire.dtl.DTLVardef@1c666cborg.highwire.dtl.DTLVardef@869b5c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

A cytoskeletal scaffold promotes motile cilia assembly by regulating transition-zone integrity

Motile cilia are eukaryotic organelles with essential chemo- and mechano-sensing functions across evolution, from single cell organisms to humans. Motile cilia of the mammalian nervous, respiratory and reproductive systems are characterized by unique motility proteins to generate fluid flow essential for transporting metabolites and removing mucus. The molecular mechanism of motile cilia biogenesis remains unknown. Here, we use mouse genetics, single-molecule motility assays, proteomics, high-resolution imaging, and in situ cryo-tomography to identify mammalian KIF27, a motor protein of the Kinesin-4 family and homologue of the Hedgehog pathway regulator COS2/KIF7, as a key regulator of motile cilia assembly. We show that KIF27 promotes the integrity of the transition zone, a diffusion barrier situated at the cilium base. Loss of KIF27 causes specific and profound defects in axonemal structure and disrupts cilia beating, which collectively lead to organismal phenotypes that recapitulate primary ciliary dyskinesia. We show that the motile properties of KIF27 are dispensable for its function in motile cilia biogenesis. Instead, KIF27 acts as a microtubule scaffold to regulate the transition zone architecture and enable correct ciliary incorporation of motility-generating proteins. Given that KIF27 homologues exist in different evolutionarily lineages, we propose that the ancestral activities of KIF27/KIF7 kinesins were to form a microtubule-associated scaffold for protein-protein interactions pertinent to cilia formation and signaling. The transition-zone associated KIF27 activities may represent a general building principle for motile cilia assembly in diverse species and cell types.

developmental biology↗

bioRxiv2025

METTL3 Aggravates Intimal Hyperplasia by Facilitating the m6A-YTHDC1-dependent SGK1 Gene Transcription

BackgroundVascular smooth muscle cell (VSMC) migration and proliferation substantially contribute to neointimal hyperplasia related to in-stent restenosis. N6-methyladenosine (m6A) catalyzed by the methyltransferase-like 3 (METTL3)-involved methyltransferase complex is the most abundant RNA epigenetic modification in eukaryotes, but the role of m6A RNA methylation in VSMC migration and proliferation as well as neointima formation remains highly controversial. MethodsPrimary human and rat VSMCs were utilized for in vitro experiments. VSMC-specific METTL3 knockout mice (Mettl3flox/floxMyh11-CreERT2) were generated to explore wire injury in carotid arteries in vivo. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) was performed to screen for target genes by METTL3-catalyzed m6A RNA methylation. Methylation site mapping, MeRIP-quantitative PCR (MeRIP-qPCR), chromatin immunoprecipitation-qPCR (ChIP-qPCR) and reporter gene assays were applied to explore how METTL3 modulates its target gene expression. ResultsMETTL3 was consistently upregulated in the neointima from mice subjected to carotid wire injury and patients undergoing carotid endarterectomy. VSMC-specific METTL3 deficiency significantly attenuated neointima formation in carotid arteries following wire injury in mice. Accordingly, METTL3 ablation markedly repressed VSMC proliferation both in vitro and in vivo. Mechanistically, METTL3 directly catalyzed m6A methylation on serum/glucocorticoid regulated kinase 1 (SGK1) mRNA and subsequently facilitated its transcription, which relies on the established association between the SGK1 transcript and SGK1 promoter DNA by recruiting the m6A reader YTHDC1. Conversely, SGK1 overexpression abolished METTL3 deficiency-mediated suppression of VSMC proliferation and postinjury neointima formation. ConclusionsMETTL3-catalyzed m6A RNA methylation promoted VSMC proliferation and aggravated postinjury neointima formation by facilitating YTHDC1-dependent SGK1 gene transcription. Targeting the METTL3-YTHDC1-SGK1 axis to modulate VSMC proliferation may be a potential strategy for in-stent restenosis therapy.

molecular biology↗

bioRxiv2025

Mitoxantrone inhibits and downregulates ERα through binding at the DBD-LBD interface

Targeting the estrogen receptor (ER or ER) through competitive antagonists, receptor downregulators, or estrogen synthesis inhibition remains the primary therapeutic strategy for luminal breast cancer. We have identified a novel mechanism of ER inhibition by targeting the critical interface between its DNA-binding domain (DBD) and ligand-binding domain (LBD). We demonstrate that mitoxantrone (MTO), a topoisomerase II inhibitor, binds at this previously unexplored DBD-LBD interface. Using comprehensive computational, biophysical, biochemical, and cellular analyses, we show that independent of its DNA damage response activity, MTO binding induces distinct conformational changes in ER, leading to its cytoplasmic redistribution and subsequent proteasomal degradation. Notably, MTO effectively inhibits clinically relevant ER mutations (Y537S and D538G) that confer resistance to current endocrine therapies, outperforming fulvestrant in both in vitro and in vivo assays. Our findings establish domain-domain interaction targeting as a viable therapeutic strategy for ER, with translational implications for other nuclear receptors.

cancer biology↗

bioRxiv2025

Cycling Molecular Assemblies for Selective Cancer Cell Golgi Disruption

The Golgi apparatus is a critical organelle responsible for intracellular trafficking and signaling, orchestrating essential processes such as protein and lipid sorting1-5. Dysregulation of its function has been implicated in various pathologies, including obesity, diabetes, and cancer, highlighting its importance as a potential therapeutic target. Despite this, the development of tools to selectively target the Golgi in specific cell types remain a significant unmet challenge in imaging and drug discovery. Golgi-specific enzyme activities, such as those mediated by protein acyltransferases and thioesterases6, offer an untapped opportunity to develop subcellularly localized therapeutics. Current approaches predominantly rely on direct protein binding but lack the necessary cell selectivity7, underscoring the unmet need for innovative strategies to selectively disrupt Golgi function in cancer cells. Here, we report the development of cycling molecular assemblies (CyMA), a novel class of small peptide derivatives (e.g., dipeptides), which exploit the unique enzymatic environment of the Golgi to establish futile cycles of reversible S-acylation. These assemblies selectively accumulate in cancer cell Golgi, interfering with protein S-acylation cycles and disrupting organelle homeostasis. CyMA impair key Golgi functions, including protein trafficking, glycosylation, and secretion, while demonstrating selective sparing hepatocytes and immune cells such as M1 macrophages. This selective activity represents a paradigm shift, utilizing an enzyme switch and leveraging intracellular environment rather than direct protein binding. Unlike conventional approaches, CyMA reduce tumor growth, drug resistance, and metastasis by pleiotropically disrupting Golgi related functions. By demonstrating the potential of futile cycles as a therapeutic strategy8, this study introduces a generalizable method for targeting organelle-specific enzyme activities. These findings not only underscore the therapeutic potential of CyMA in cancer but also pave the way for future applications in other Golgi-associated diseases.

biochemistry↗

bioRxiv2025

The mycomembrane differentially and heterogeneously restricts antibiotic permeation

The recalcitrance of Mycobacterium tuberculosis to antibiotic treatment has been broadly attributed to the impermeability of the organisms outer mycomembrane. However, the studies that support this inference have been indirect and/or reliant on bulk population measurements. We previously developed the Peptidoglycan Accessibility Click-Mediated AssessmeNt (PAC-MAN) method to covalently trap azide-modified small molecules in the peptidoglycan cell wall of live mycobacteria, after they have traversed the mycomembrane. Using PAC-MAN we now show that the mycomembrane differentially restricts access of fluorophores and antibiotic derivatives. Mycomembranes of both M. tuberculosis and the model organism M. smegmatis discriminate between divergent classes of antibiotics as well as between antibiotics within a single family, the fluoroquinolones. By analyzing sub-populations of M. tuberculosis and M. smegmatis, we also found that some fluorophores and vancomycin are heterogeneously restricted by the mycomembrane. Our data indicate that the mycomembrane is a molecule- and cell-specific barrier to antibiotic permeation. Abstract Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/630956v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@4bdeb7org.highwire.dtl.DTLVardef@10ade47org.highwire.dtl.DTLVardef@872dceorg.highwire.dtl.DTLVardef@d04b59_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Benchmarking the coding strategies of non-coding mutations on sequence-based downstream tasks with machine learning

Non-coding single nucleotide polymorphisms (SNPs) are key modulators of gene regulation and have been implicated in diverse complex traits and diseases. With the growing demand for accurate functional interpretation of non-coding variants, the choice of encoding strategies becomes critical in downstream predictive modeling. Despite recent advances, a systematic evaluation of encoding approaches tailored for non-coding SNPs remains lacking. To address this gap, we present a comprehensive benchmark that evaluates six representative encoding strategies, including categorical, semantic, and functional embeddings, across three quantitative trait loci (QTL)-related prediction tasks. The study encompasses nine machine learning and deep learning models and incorporates experimental controls and repeated trials to ensure robustness and reproducibility. We assess each strategy along multiple dimensions, such as interpretability, representation abundance, and computational efficiency. Rather than ranking individual methods, our analysis emphasizes the interaction between encoding strategies, model types, and preprocessing protocols, and highlights their collective influence on predictive performance. This work establishes a standardized framework for evaluating non-coding SNP representations and offers actionable guidance for selecting and optimizing prediction pipelines in regulatory genomics.

bioinformatics↗

bioRxiv2024

A new class of penicillin-binding protein inhibitors to address drug-resistant Neisseria gonorrhoeae

{beta}-Lactams are the most widely used antibiotics for the treatment of bacterial infections because of their proven track record of safety and efficacy. However, susceptibility to {beta}-lactam antibiotics is continually eroded by resistance mechanisms. Emerging multidrug-resistant (MDR) Neisseria gonorrhoeae strains possessing altered penA alleles (encoding PBP2) pose a global health emergency as they threaten the utility of ceftriaxone, the last remaining outpatient antibiotic. Here we disclose a novel benzoxaborinine-based penicillin-binding protein inhibitor series (boro-PBPi) that is envisioned to address penA-mediated resistance while offering protection against evolution and expansion of {beta}-lactamases. Optimization of boro-PBPi led to the identification of compound 21 (VNRX-14079) that exhibits potent antibacterial activity against MDR N. gonorrhoeae achieved by high affinity binding to the PBP2 target. Boro-PBPi/PBP2 complex structures confirmed covalent interaction of the boron atom with Ser310 and the importance of the {beta}3-{beta}4 loop for improved affinity. 21 elicits bactericidal activity, a low frequency of resistance, a good safety profile, suitable pharmacokinetic properties, and in vivo efficacy in a murine infection model against ceftriaxone-resistant N. gonorrhoeae. 21 is a promising anti-gonorrhea agent poised for further advancement.

microbiology↗

bioRxiv2024

Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms

Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. To address this, we collected clinical samples from three cancer types - colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer - and generated serial tissue sections for systematic evaluation. Using these uniformly processed samples, we generated spatial transcriptomics data across five high-throughput platforms with subcellular resolution: Stereo-seq v1.3, Visium HD FFPE, Visium HD FF, CosMx 6K, and Xenium 5K. To establish ground truth datasets, we profiled proteins from adjacent tissue sections corresponding to all five platforms using CODEX and performed single-cell RNA sequencing on the same samples. Leveraging manual cell segmentation and detailed annotations, we systematically assessed each platforms performance across key metrics, including capture sensitivity, specificity, diffusion control, cell segmentation, cell annotation, spatial clustering, and transcript-protein alignment with adjacent CODEX. The uniformly generated, processed, and annotated multi-omics dataset is valuable for advancing computational method development and biological discoveries. The dataset is accessible via SPATCH, a user-friendly web server for visualization and download (http://spatch.pku-genomics.org/).

genomics↗

bioRxiv2024

Infectivity of a pathogenicity-attenuated Chlamydia muridarum mutant in the genital tract

A C. muridarum mutant designated as intrOv was evaluated as an intracellular Oral vaccine vector because it can induce protection in the genital tract following oral inoculation but does not elicit genital pathology following intravaginal infection. However, the mechanism of intrOvs attenuation is unclear. Here we report that few live organisms were recovered from vaginal swabs during the early stage of intrOv intravaginal infection in mice. At a low inoculating dose, an isogenic wild-type control strain established a productive infection, while intrOv failed to do so. Although a higher inoculating dose allowed intrOv and its control to productively infect mice, fewer live intrOv than the control organisms were recovered from the lower genital tract tissues on day 3 post-infection. By day 7, animals infected with intrOv or the control shed similar numbers of live organisms, suggesting the intrOvs deficiency on day 3 was transient. Consistently, intrOv reduced invasion of epithelial cells but maintained as robust intracellular replication as its control. Our results correlate intrOvs delay in infecting the lower genital tissues and reduction in invading epithelial cells with its attenuation in genital pathogenicity, laying the foundation for further revealing the mechanisms of the intrOvs attenuation in pathogenicity during genital tract infection.

microbiology↗

bioRxiv2024

Spatiotemporal Regulatory Logics of Mouse Gastrulation

Spatiotemporal coordination of cellular and molecular events is crucial for cell fate commitment during mouse gastrulation. However, the high-precision mechanisms governing the timing and spatial dynamics remain poorly understood. Here, we present a time-series single-cell multi-omic dataset from the mouse gastrulating embryos and construct a hierarchical gene regulatory landscape. Integrating this with real three-dimensional transcriptomic coordinate, we created ST-MAGIC and ST-MAGIC (+) atlas, dissecting the spatiotemporal logics of regulatory networks and signaling responsiveness underpinning the lineage commitment at gastrulation. Specifically, we delineated the multi-omic basis for left-right symmetry breaking events in the gastrula and also revealed the spatiotemporal molecular relay for axial mesendoderm lineage, where early and intermediate transcription factors first open the chromatin regions and setup the responsiveness to signaling, followed by terminal factors to consolidate the transcriptomic architecture. In summary, our study presents a spatiotemporal regulatory logic framework of mouse gastrulation, that advances our understanding of mammalian embryogenesis.

developmental biology↗

bioRxiv2024

Differential metabolic biomarkers between coronary heart disease and diabetes mellitus

BackgroundCoronary heart disease (CHD), the leading cause of death globally, is a complex disease often association with metabolic disorders, particularly when co-occurring with diabetes mellitus (DM). However, the mechanisms underlying the interaction between these two chronic conditions remain poorly understood. MethodsIn this study, we enrolled 320 participants, including 103 healthy controls (HC), 62 individuals with CHD, 44 with DM, and 47 with both CHD and DM (CHDDM)) in the training set, along with 64 participants (20 HC, 18 CHD, 12 DM, and 14 CHDDM) in the test set. Plasma metabolomic profiling was performed using gas chromatograph-mass spectrometry (GC-MS) and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS)-based multi-platform untargeted metabolomics. ResultsUsing multi-platform metabolomics, we identified 453 distinct metabolites. Through multivariate statistical analysis, we assigned 63, 27, and 56 disease-associated metabolic biomarkers for CHD, DM, and CHDDM, respectively, followed by pathway enrichment analysis. Using an area under the receiver operating characteristic (ROC) curve (AUC) cutoff value > 0.77, we identified 10, 4, and 8 disease-specific biomarkers for CHD, DM, and CHDDM, respectively. Notably, N-Formyl-L-methionine, N-Acetyl-L-methionine, PE 36:1p (18:0p/18:1), PE 36:2p (18:0p/18:2), and PE 34:2p (16:0p/18:2) were predominant in CHD, glycerophosphocholine and turanose were distinctive to DM, and xanthine and PE 38:5p (18:1p/20:4) were unique to CHDDM. These disease-specific metabolites showed superior diagnostic performance in their respective conditions. Additionally, 23 metabolites were identified as potential biomarkers for assessing the risk of CHD in DM patients. ConclusionThis comparative metabolomics approach provided new insights into disease-specific markers and pathogenic pathways, offering potential for improved diagnosis and management of CHD and DM.

molecular biology↗

bioRxiv2024

In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens

Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.

microbiology↗

bioRxiv2024

Bacterial lipoate protein ligases rescue lipoylation and respiration deficiency in mammals

Human lipoylation pathway deficiencies caused by LIPT2/LIAS/LIPT1 gene mutations lead to inherited metabolic disorders characterized by severe defects of mitochondrial energy and amino acids metabolism. Patients with such mutations suffer from hyperlactic acidemia, encephalopathy, hypotonia and early death. So far there is no effective treatment. Here we introduced the bacteria salvage lipoylation pathway, which is absent in eukaryotes, into lipoylation defective human cells and mouse models. Both E. coli-derived LplA and B. subtilis-derived LplJ restored the phenotypes of LIPT2/LIAS/LIPT1 gene knockout cells to those of wildtype cells with lipoic acid supplementation. Biochemical and isotope tracing analysis demonstrated LplA and LplJ function through direct lipoylation of the H protein of glycine cleavage system and the E2 subunits of 2-oxoacid dehydrogenases, thereby reactivating the short-circuited TCA cycle and amino acids metabolism. This strategy is further extended to treat lipoyl precursor supply defects caused by MECR and FDX1 mutations and its efficacy and safety are validated in Lipt1-/- and LplAOE/+ mouse models. This study provides systematic characterization of lipoylation deficiency and paves the way to gene therapy for treatment of lipoylation-deficient patients.

cell biology↗