Biology subjects

Wu, G.

Publications and source records attributed to Wu, G..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Pcbp1 orchestrates amino acid metabolism burst during the naive-to-primed pluripotency transition

Embryo implantation is accompanied by the naive-to-primed pluripotency transition in epiblast cells, making them receptive to external differentiation signals. In addition to this developmental program switch, implantation suggests that an anabolic boost is required for this process, as the embryo-uterine connection begins supplying the requisite nutrients. In this study, we show that the DNA-binding protein Pcbp1 plays a key role in intensifying amino acid metabolism during the priming of pluripotent stem cells. Knockout of the Pcbp1 gene leads to embryo growth arrest a few days after implantation. By modeling the naive-to-primed pluripotency transition in vitro, we observe reduced proliferation and induction of apoptosis in cells deficient for Pcbp1. Using multi-omics approaches, we uncover a crucial role for Pcbp1 in driving a transcriptional burst of numerous genes involved in the import and the de novo synthesis of essential and conditionally essential amino acids. Pcbp1 deficiency is consequently associated with a slowdown in protein biosynthesis, explaining the early lethal phenotype of knockout embryos. Our findings thus uncover the molecular mechanisms underlying anabolic changes during the naive-to-primed pluripotency transition and highlight the essential role of Pcbp1 in this process, also pointing to its functions in highly proliferative cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/658314v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1e17b48org.highwire.dtl.DTLVardef@64e940org.highwire.dtl.DTLVardef@10d6b00org.highwire.dtl.DTLVardef@1ec0d23_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

The anaerobic WOR-3 Bacteria: Hydrogenotrophic metabolism and unique carbon fixation via Archaeal form III RuBisCO

The uncultured WOR-3 phylum is widely distributed in anaerobic environments, including hot springs, marine ecosystems, and hydrothermal vents, yet its ecological roles and metabolic capabilities remain poorly understood. In this study, we analyzed 180 medium- to high-quality metagenome-assembled genomes (MAGs), including 59 newly reconstructed from environmental samples and 121 retrieved from the Genome Taxonomy Database (GTDB). Phylogenetic analyses resolved the WOR-3 lineage into four subgroups (subgroup 1-4). Metabolic reconstruction revealed significant divergence of the carbon, sulfur, nitrogen and hydrogen metabolism pathways among the different subgroups. Subgroup 1 was characterized by fermentative metabolism involving formate and ethanol, and uniquely exhibited potential for carbon fixation via Calvin cycle, as indicated by the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene. Notably, WOR-3 RuBisCO is phylogenetically affiliated with archaeal form III, although the carbon fixation pathway follows the canonical bacterial Calvin cycle--a feature of potential evolutionary significance. Subgroup 3 exhibits metabolic versatility, including genes for dissimilatory sulfate reduction, sulfur oxidation, partial denitrification, and fatty acid degradation. In addition, all subgroups harbored key components of hydrogen metabolism, including widespread NiFe hydrogenases and Rnf complexes, supporting H2-dependent electron transfer and energy conservation under anaerobic conditions. Featuring near-universal presence of complexes I and II and frequent occurrence of terminal oxidases (cydAB and coxABC)--suggests a facultative anaerobic lifestyle. Collectively, this study expands the genomic framework for the WOR-3 phylum and provides novel insights into the metabolic versatility and ecological functions of this previously uncharacterized lineage in biogeochemical cycles of carbon, nitrogen, and sulfur. IMPORTANCEThe WOR-3 phylum represents a widespread but poorly understood bacterial lineage inhabiting diverse anaerobic/microaerobic environments. By integrating 180 metagenome-assembled genomes, including 59 newly reconstructed, this study provides the most comprehensive genomic framework to date for WOR-3. Phylogenomic and metabolic analyses revealed four distinct subgroups with divergent capacities for carbon, sulfur, and nitrogen metabolism. Notably, subgroup 1 encodes a complete Calvin-Benson-Bassham (CBB) cycle featuring an archaeal-type form III RuBisCO, suggesting an unusual evolutionary trajectory for carbon fixation in this lineage. Subgroup 3 exhibits versatile metabolic potential, including dissimilatory sulfur metabolism, partial denitrification, and fatty acid degradation, highlighting its possible roles in multiple biogeochemical processes. The widespread presence of hydrogenases and respiratory complexes across all subgroups supports energy conservation under anaerobic or microaerobic conditions. These findings not only expand the taxonomic and functional landscape of the WOR-3 phylum but also offer key insights into its ecological roles in global element cycling.

microbiology↗

bioRxiv2025

Bridging Genomics and Clinical Medicine: RSVrecon Enhances RSV Surveillance with Automated Genotyping and Clinically-important Mutation Reporting

BackgroundRespiratory Syncytial Virus (RSV) causes significant respiratory infections, particularly in young children and elderly adults. Genetic variations in the fusion (F) protein can reduce the efficacy of vaccination and monoclonal antibody treatments, emphasizing the need for genomic surveillance of this virus. MotivationCurrent pipelines for RSV genome assembly focus on sequence reconstruction but often lack features for detecting genotypes, clinically relevant mutations, or presenting results in formats that are suitable for clinical researchers. ResultsWe introduce RSVrecon, an advanced bioinformatics pipeline for comprehensive RSV genome assembly and phylogenetic analysis. RSVrecon processes raw FASTQ files into annotated variant reports and delivers results in multiple formats (CSV, PDF, HTML) tailored to diverse end users. A key innovation of RSVrecon is not only its integrated detection of clinically critical features--including genotype classification and F protein mutation calling, capabilities absent in most analytical pipelines--but also its presentation of these results to clinicians via an integrated, graphical, and user-friendly interface. Its modular design, powered by Nextflows modern framework, ensures a scalable and robust workflow, while user-friendly reports enable seamless translation of genomic data into actionable clinical insights. Benchmarking against existing pipelines using clinical datasets revealed that RSVrecon achieves comparable genomic assembly accuracy while excelling in three key dimensions: (1) expanded functional capabilities, (2) intuitive biological interpretation of the results, and (3) superior user experience and accessibility. By seamlessly translating RSV genomic data into clinically meaningful information, RSVrecon empowers research breakthroughs, guides clinical care decisions, and strengthens surveillance systems. With these features, RSVrecon offers an enhanced approach to RSV surveillance and research. The tool is freely available at https://github.com/stjudecab/rsvrecon and https://github.com/stjudecab/RSVreconPy. Key PointsO_LIRSVrecon enables comprehensive clinical detection for RSV such as identifying genotypes and F protein mutations. C_LIO_LIRSVrecon delivers results through an integrated, graphical, and user-friendly interface for clinicians. C_LIO_LIRSVrecons Nextflow-based design ensures robust, scalable, and consistent performance. C_LIO_LIRSVrecon matches assembly accuracy while excelling in functionality, interpretation, and accessibility during benchmarking. C_LI

bioinformatics↗

bioRxiv2025

Gut miRNA regulates gut microbiome and Alzheimer pathology in App-knock-in mice

Alzheimers disease (AD) alters the gut microbiome. It remains unclear whether manipulation of miRNA could modulate the gut microbiome and AD pathologies. Depletion of gut miRNA in App-knock-in mice by conditional knockout of Dicer1 gene in intestinal epithelial cells: 1) decreased the absolute number and changed the composition of bacteria in both the gut and brain; 2) reduced cerebral A{beta} load by inhibiting {beta}-secretase activity and increasing the expression of LRP1 and ABCB1 at the blood-brain barrier; 3) increased Il-10 transcription and decreased the transcription of Ccl-2 gene, and that of Ndufa2 and Ndufa5 genes encoding mitochondrial respiratory enzymes in the brain; and 4) induced anxiety symptoms without affecting cognitive function in AD mice. Thus, manipulating miRNA in the gut can modify AD pathogenesis. Future studies should focus on identifying AD-specific miRNAs in the gut that can be therapeutically exploited (e.g. by oral administration) to prevent the progression of AD.

neuroscience↗

bioRxiv2025

A novel tool for labeling intermediary proteins between two non-interacting proteins

Decoding the complexities of signaling pathways is fundamental for deciphering the mechanisms underlying tissue development, homeostasis, and disease pathogenesis. Proximity labeling tools have been instrumental in identifying upstream or downstream effectors of specific proteins within signaling pathways. However, currently, there are no tools available to directly label and capture intermediary proteins that bridge two non-interacting proteins. Here, we developed STUPPIT (Split-TurboID and PUP-IT based Protein Identification Tool), a novel method combining split-TurboID and PUP-IT to biotinylate intermediary proteins of two non-interacting proteins through a two-step enzymatic reaction. Two approaches of STUPPIT were validated using three well-characterized protein triad, including YAP1/AMOT/{beta}-actin, YAP1/LATS1/MOB1A, and {beta}-catenin/-catenin/{beta}-actin. Combining STUPPIT and proteomics, we identified novel intermediary proteins including RNF20, ERC1, USP7 and TRIM33, which interact both with {beta}-catenin and SMAD4, key components of the Wnt and BMP signaling pathways. In conclusion, STUPPIT represents a powerful tool for labeling and capturing intermediary proteins between non-interacting partners, offering new insights into protein-protein interactions and advancing signal transduction research.

cell biology↗

bioRxiv2025

Identification of immune-mitophagy related gene in PD based on single-cell sequencing and Mendelian randomization

Parkinsons disease (PD) involves dysregulated mitophagy and immuneresponses, though the underlying mechanisms remain unclear. To identify key genes linking these pathways, we integrated single-cell RNA sequencing (GSE157783) with Mendelian randomization(MR) analysis, screening mitophagy-related genes (MRGs) and immune-related genes (IRGs). Differential expression analysis across PD cell subpopulations, combined with MR, revealed four causal genes: SLC11A1and DDX17(protective) and MRAS and PDIA3(risk). These genes were enriched in antigen presentation and calcium signaling pathways and exhibited dynamic expression in astrocytes and microglia during differentiation. Subsequent protein-protein interaction(PPI) network, regulatory (SCENIC), and drug-target analyses further characterized their roles. Validation in MPTP-induced PD mice confirmed behavioral deficits and altered expression of these genes, supporting their functional relevance. Our findings highlight SLC11A1, DDX17, MRAS, and PDIA3 as critical mitophagy-immune hubs in PD, offering mechanistic insights and therapeutic targets. Author SummaryPD is a neurodegenerative disorder linked to mitochondrial dysfunction (mitophagy) and immune dysregulation, yet the interplay between these mechanisms remains poorly understood. Using integrative single-cell sequencing and MR analyses, we identified four key genes-SLC11A1, DDX17, MRAS, and PDIA3-that bridge immune and mitophagy pathways in PD pathogenesis. These genes exhibit causal relationships with PD risk, offering novel insights into diagnostic and therapeutic strategies.

genetics↗

bioRxiv2025

Unveiling the pathogenicity of Cunninghamella echinulata SMH-1 and its bioactive metabolites through metabolomics: Dual-action disruption of Solenopsis invicta mitochondrial bioenergetics and cuticular integrity

The invasive red imported fire ant, Solenopsis invicta, poses significant ecological and economic challenges, necessitating sustainable alternatives to conventional pest control. This study evaluates the biocontrol potential of Cunninghamella echinulata isolate SMH-1, an entomopathogenic fungus, through integrated morphological, biochemical, and metabolomic analyses. Light and scanning electron microscopy elucidated infection dynamics, revealing conidial germination, cuticular penetration, and systemic hyphal proliferation, culminating in complete cadaver colonization. At 1x10 conidia/mL, SMH-1 achieved 100% mortality in S. invicta workers within 7 days, with virulence maintained across thermal gradients (10-30{degrees}C). Acetone extracts of SMH- 1 induced dose-dependent lethality, reaching 100% mortality at 1,000 mg/L. Nineteen significantly differentiated metabolites were identified from phospholipids category through UPLC/MS analysis of isolate SMH-1. The derived compounds also showed strong potential against S. invicta, among which dihydrocoumarin caused 100% mortality over 12-days of exposure. The bioactivity of isolate SMH-1 (Conidia), (extracts) and (dihydrocoumarin) against S. invicta revealed significantly differentiated metabolites as (Sulfolithocholylglycine, PE(18_1(9Z)_0_0), CE(12:0), LysoPI(18:1(9Z)/0:0) and Hydroxydestruxin B), (Tropine, lignoceric acid, 9-deoxy-9-methylene-16,16-dimethyl-PGE2, Flecainide and Jubanine B), and (3-O-alpha-D-Glucopyranuronosyl-D-xylose, Rilmakalim, 2-Amino-3-methyl-1-butanol, 2,4-Dimethyl-1,3-oxazole-5-carboxylic acid and Caffeinol), respectively. Citrate cycle (TCA) was significantly impacted by differential expression of pyruvate, pyruvic acid, succinic acid and fumaric acid. These findings underscore SMH-1s multifaceted biocontrol potential, combining direct pathogenicity, thermo-tolerance, and metabolite-mediated toxicity. By delineating host-pathogen interactions and metabolic disruptions, this work advances C. echinulata isolate SMH-1 as a sustainable candidate for integrated S. invicta management, offering an eco-friendly alternative to synthetic insecticides. Author SummaryInvasive fire ants (S. invicta) threaten ecosystems and agriculture worldwide, and current chemical controls often harm the environment. In this study, we explored a natural alternative: a soil-dwelling fungus called Cunninghamella echinulata (strain SMH-1). We discovered that this fungus can kill fire ants with remarkable efficiency. When applied directly, its spores caused 100% ant mortality within a week, even under varying temperatures. We also identified key fungal compounds, including dihydrocoumarin, which are lethal to ants. By studying how the fungus invades and disrupts the ants biology-such as breaking down their protective outer layers and interfering with their energy production, we revealed why SMH-1 is so effective. Our findings highlight SMH-1s potential as a safe, eco-friendly biocontrol agent. This fungus could reduce reliance on synthetic pesticides, offering farmers and communities a sustainable tool to combat fire ant invasions while protecting biodiversity. Our work bridges lab discoveries and real-world pest management, paving the way for greener solutions in agriculture and ecosystem conservation.

microbiology↗

bioRxiv2025

MitoEdit: a pipeline for optimizing mtDNA base editing and predicting bystander effects

Short Structured AbstractO_ST_ABSMotivationC_ST_ABSHuman mitochondrial DNA (mtDNA) mutations are causally implicated in maternally inherited mitochondrial respiratory disorders; however, the role of somatic mtDNA mutations in both late-onset chronic diseases and cancer remains less clear. Although recent advances in mtDNA base editing technology have the potential to model and characterize many of these mutations, current editing approaches are complicated by the potential for multiple unintentional edits (bystanders) that are only identifiable through empirical trial and error, thereby sacrificing valuable time and effort towards suboptimal construct development. ResultsWe developed MitoEdit, a novel tool that incorporates empirical base editor patterns to facilitate identification of optimal target windows and potential bystander edits. MitoEdit allows users to input DNA sequences in a text-based format, specifying the target base position and its desired modification. The program generates a list of candidate target windows with a predicted number of bystander edits and their functional impact, along with flanking nucleotide sequences designed to bind TALE (transcription activator-like effectors) array proteins. In silico evaluations indicate that MitoEdit can predict the majority of bystander edits, thereby reducing the number of constructs that need to be tested empirically. To the best of our knowledge, MitoEdit is the first tool to automate prediction of base edits. Availability and implementationMitoEdit is freely available at Kundu Lab GitHub (https://github.com/Kundu-Lab/mitoedit). ContactCorresponding email: Gang.Wu@stjude.org; Mondira.Kundu@stjude.org Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2025

Kynurenine Metabolism is Associated with Antidepressant Response to Selective Serotonin Reuptake Inhibitors

Alterations in the kynurenine pathway, and in particular the balance of neuroprotective and neurotoxic metabolites, have been implicated in the pathophysiology of Major Depressive Disorder (MDD) and antidepressant treatment response. In this study, we examined the relationship between changes in kynurenine pathway activity (Kynurenine/Tryptophan ratio), focusing on the balance of neuroprotective-to neurotoxic metabolites (Kynurenic Acid/Quinolinic Acid and Kynurenic Acid/3-Hydroxykynurenine ratios), and response to 8 weeks of selective serotonin reuptake inhibitor (SSRI) treatment, including early changes four weeks after SSRI initiation. Additionally, we examined relationships between kynurenine metabolite ratios and three promising biomarkers of depression and antidepressant response: amygdala/hippocampal volume, and glutamate metabolites in the anterior cingulate cortex. Responders showed an increase in the Kynurenic Acid/3-Hydroxykynurenine ratio by week 8 (F(1,46) = 11.92, p = .001) and early increases in the Kynurenine/Tryptophan ratios at week 4 (F(2,58) = 5.224, p = .008), while Non-Responders did not. Pre-treatment Kynurenic Acid/Quinolinic Acid and Kynurenic Acid/3-Hydroxykynurenine ratios were positively associated with right amygdala volume ({beta} = . 247 p = .032 and {beta} = .245 p = .028, respectively). Lastly, in a subset of participants, pre-treatment Kynurenic Acid/3-Hydroxykynurenine ratio showed a positive, small effect size association with glutamate metabolites (Glx) in the anterior cingulate cortex ({beta} = .307 p = .079), which became significant post-treatment with a large effect size ({beta} = .652 p = .021). These results suggest that response to SSRIs may arise from shifting the balance from neurotoxic to neuroprotective kynurenine metabolites.

neuroscience↗

bioRxiv2024

Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding

Allosteric regulation allows proteins to dynamically respond to environmental cues by modulating activity at sites away from the catalytic center. Despite its importance, the SET-domain protein lysine methyltransferase superfamily has been understudied. Here, we present four crystal structures of SMYD2, a unique family member with a MYND domain. Our findings reveal a novel allosteric binding site with high conformational plasticity and promiscuity, capable of binding peptides, proteins, PEG, and small molecules. This site exhibits positive cooperativity with substrate binding, influencing catalytic activity. Mutations here significantly alter substrate affinity, changing the enzymes kinetic profile. Specificity studies show interaction with PARP1 but not histones, suggesting targeted regulation. Interestingly, this sites function remains unaffected by active site changes, indicating unidirectional mechanisms. Our discovery provides novel insights into SMYD2s biochemical regulation and lays the foundation for broader research on allosteric control in lysine methyltransferases. Given SMYD2s role in various cancers, this work opens exciting avenues for designing specific allosteric inhibitors with reduced off-target effects.

biochemistry↗

bioRxiv2024

Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use

Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most widely used medications for the management of chronic pain; however, they are associated with numerous gastrointestinal (GI) adverse events. Although many mechanisms have been suggested, NSAID-induced enteropathy has been thought to be primarily due to inhibition of both cyclooxygenases (COX) -1 and -2, which results in suppression of prostaglandin synthesis. Yet surprisingly, we found that concomitant postnatal deletion of Cox-1 and -2 over 10 months failed to cause intestinal injury in mice unless they were treated with naproxen or its structural analog, phenylpropionic acid, which is not a COX inhibitor. Cox double knockout mice exhibit a distinct gut microbiome composition and cohousing them with controls rescues their dysbiosis and delays the onset of NSAID-induced GI bleeding. In both the UK Biobank and All of Us human cohorts, coadministration of antibiotics with NSAIDs is associated with an increased frequency of GI bleeding. These results show that prostaglandin suppression plays a trivial role in NSAID-induced enteropathy. However, Cox deletion causes dysbiosis of the gut microbiome that amplifies the enteropathic response to NSAIDs.

pharmacology and toxicology↗

bioRxiv2024

P450-Catalyzed Biaryl Macrocyclization of Leaderless Ribosomal Peptides

Macrocyclic peptides containing biaryl motifs, predominantly derived from natural products, are valuable scaffolds due to their structural rigidity and potent bioactivity. However, current synthetic methods remain constrained by the absence of broadly applicable strategies across chemocatalytic and biocatalytic platforms. Here, we discover a versatile P450 enzyme, GpeC, capable of facilitating oxidative C-C/O/N cross-coupling for peptide biaryl macrocyclization (PBC) with leader-independent activity. Crystal structure analysis of GpeC rationalizes leader-independent property and reveals adaptive recognition that enables access to diverse biaryl-linked macrocycles. GpeC exhibits exceptional substrate promiscuity, accommodating 19 of 20 canonical amino acids and diverse noncanonical analogs within a minimal tetrapeptide scaffold. The efficient semi-synthesis of the natural product Rubrin further demonstrated the versatility of GpeC. We further introduced lytic to tetraregion (LTT), a one-step, single enzyme synthesis for modular synthesis of biaryl-cyclized tetrapeptide. Overall, GpeCs robustness and programmability position it as a broadly applicable biocatalyst for the synthesis of biaryl macrocyclic peptides.

biochemistry↗

bioRxiv2024

Ex vivo and in vivo HIV-1 latency reversal by Mukungulu, a protein kinase C-activating African medicinal plant extract

Current HIV latency reversing agents (LRAs) have had limited success in clinic, indicating the need for new strategies that can reactivate and/or eliminate HIV reservoirs. "Mukungulu," prepared from the bark of Croton megalobotrys Mull. Arg., is traditionally used for HIV/AIDS management in Northern Botswana despite containing an abundance of protein kinase C (PKC)-activating phorbol esters ("namushens"). Here we show that Mukungulu is tolerated in mice at up to 12.5 mg/kg while potently reversing latency in antiretroviral therapy (ART)-suppressed HIV-infected humanized mice at 5 mg/kg. In peripheral blood mononuclear cells (PBMC) and isolated CD4+ T-cells from ART-suppressed people living with HIV-1, 1 {micro}g/mL Mukungulu reverses latency on par with or superior to anti-CD3/CD28 positive control, as measured by HIV gag-p24 protein expression, where the magnitude of HIV reactivation in PBMC corresponds to intact proviral burden levels in CD4+ T-cells. Bioassay-guided fractionation identifies 5 namushen phorbol ester compounds that reactivate HIV expression, yet namushens alone do not match Mukungulus activity, suggesting additional enhancing factors. Together, these results identify Mukungulu as a robust natural LRA which may warrant inclusion in future LRA-based HIV cure and ART-free remission efforts.

microbiology↗

bioRxiv2024

G3BP1 Maintains Vascular Endothelial Barrier Integrity by Negatively Regulating the MYD88-ARNO-ARF6 Signaling Pathway

Endothelial permeability is essential for vascular function. This process is regulated by intercellular junctions, including adherens junctions (AJs) and tight junctions (TJs), which form the endothelial barrier and dynamically connect adjacent cells. However, the mechanisms that control endothelial permeability are not fully understood. We investigated the role of the RNA-binding protein G3BP1 in regulating endothelial permeability. We examined the effects of Loss of g3bp1 in conditional knockout mice and primary human HUVEC cells. We analyzed endothelial barrier integrity and permeability, focusing on AJ and TJ expression, under both normal and LPS-induced inflammatory conditions. Loss of g3bp1 in vascular endothelial cells decreased AJ and TJ expression, compromised barrier integrity, and increased permeability. These effects were exacerbated under LPS-induced inflammatory conditions. Loss of g3bp1 also increased the expression of MYD88, ARNO, and ARF6, and enhanced ARF6 activity. Mechanistically, G3BP1 bound to and stabilized MYD88 mRNA, negatively regulating the MYD88-ARNO-ARF6 signaling pathway. Inhibiting this pathway by reducing MYD88 or ARF6 expression, or inhibiting ARNO activity, restored AJ/TJ expression and barrier function in G3BP1-deficient models. Our findings identify G3BP1 as a novel regulator of vascular endothelial permeability. G3BP1 acts by negatively regulating the MYD88-ARNO-ARF6 signaling pathway. Targeting G3BP1 may be a potential therapeutic strategy for diseases associated with endothelial barrier dysfunction.

physiology↗

bioRxiv2024

Systematically investigating and identifying unmodified bacteriocins in the human gut microbiome

Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with being niche-specific and enriched in the human microbiome. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.

microbiology↗

bioRxiv2024

The effects of 17α-estradiol treatment on endocrine system revealed by single-nucleus transcriptomic sequencing of hypothalamus

In this study, we investigated 17-estradiols role in lifespan extension from long-term administration. Pooled hypothalami from aged male Norway brown rats treated with 17-estradiol (O.T), aged male controls (O), and young male controls (Y) underwent single-nucleus transcriptomic sequencing (snRNA-seq). To evaluate the effects of 17-estradiol on aging neurons, supervised clustering of neurons based on neuropeptides and their receptors were used to evaluate the responses of each neuron subtype during aging and after 17-estradiol treatment. The elevated cellular metabolism, stress and decreased expression levels of pathways involved in synapse formation in neurons initiated by aging were significantly attenuated by 17-estradiol. Assessment of changes in neuron populations showed that neurons related to food intake, reproduction, blood pressure, stress response, and electrolyte balance were sensitive to 17-estradiol treatment. 17-estradiol treatment not only increased serum Oxytocin (Oxt), but also heightened the activity of hypothalamic-pituitary-gonadal (HPG) axis, as evidenced by significantly elevated levels of plasma Gnrh, total testosterone, and decreased estradiol. Elevated Gnrh1 was confirmed to be one of the causal effects mediating the role of 17-estradiol in energy homeostasis, neural synapse, and stress response. Notably, Crh neurons exhibited prominent stressed phenotype in O.T, distinct to appetite-stimulating neurons Agrp and Ghrl. Therefore, the HPG axis and energy metabolism may be key targets of 17-estradiol in male hypothalamus. Additionally, supervised clustering of neurons was shown to be a useful method for assessing treatment responses and cellular perturbation among different neuron subtypes in the hypothalamus.

neuroscience↗

bioRxiv2024

The long-chain fatty acid-CoA ligase FadD1 monitors Pseudomonas aeruginosa quorum sensing as a receptor of cis-2-decenoic acid

Diffusible signal factor (DSF)-family quorum sensing (QS) signals are widely utilized by many bacterial pathogens to modulate various biological functions and virulence. Previous studies showed that cis-2-decenoic acid (cis-DA) is involved in modulation of biofilm dispersion in Pseudomonas aeruginosa, but its signaling mechanism remains vague. Here, we report that cis-DA regulates the physiology and virulence of P. aeruginosa through the long-chain fatty acid-CoA ligase FadD1. Cis-DA specifically binds to FadD1 with high affinity and enhances the binding of FadD1 to the promoter DNA region of lasR. Further analysis showed that the FadD1 is a response regulator of cis-DA with a DNA-binding leucine zipper motif to control the transcription of various target genes. Moreover, FadD1 exhibited catalytic activity on cis-2-dodecenoic acid (BDSF) of Burkholderia cenocepacia and enhanced the competitiveness of P. aeruginosa. Together, our work presents a new DSF-type QS signaling system, which is highlighted by its receptor and response regulator evolved from a canonical enzyme of fatty acid metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/598097v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@66b8aaorg.highwire.dtl.DTLVardef@1e5b9b9org.highwire.dtl.DTLVardef@1043525org.highwire.dtl.DTLVardef@13d3ed1_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsThe long-chain fatty acid-CoA ligase FadD1 acts as a global transcriptional regulator in P. aeruginosa. FadD1 is a receptor of QS signal cis-DA and functions at the top of the QS hierarchy in P. aeruginosa. The homolog of FadD1 in P. fluorescens could bind to the target gene promoter by responding to cis-DA. In briefPseudomonas aeruginosa is a human pathogen with antibiotic resistance and a wide range of dynamic defenses makes it an extremely challenging organism to treat in modern-day medicine. It employs cis-2-decenoic acid (cis-DA) quorum sensing to regulate the physiology and pathogenesis. Song et al. demonstrate that the long-chain fatty acid-CoA ligase FadD1 controls the important biological functions and virulence in P. aeruginosa as a novel response regulator of cis-DA signal.

microbiology↗

bioRxiv2024

The Transcription Factor OsNAC5 Mediates Cadmium Stress Response and Accumulation in Rice

Cadmium (Cd) is a toxic heavy metal that endangers human health through contaminated rice consumption. Reducing Cd uptake in rice is essential for minimizing grain Cd accumulation. However, the transcriptional regulation of Cd uptake in rice remains largely elusive. This study reveals that the transcription factor OsNAC5 in Oryza sativa positively regulates the Cd transporter gene OsNRAMP1, influencing Cd uptake. OsNAC5 is primarily expressed in roots, localized to the nucleus, and upregulated by Cd-induced H2O2. Knocking out OsNAC5 reduces Cd levels in both shoots and roots and increases Cd sensitivity. OsNRAMP1 expression, enhanced by Cd stress, depends on OsNAC5, which binds to "CATGTG" motifs in the OsNRAMP1 promoter activating its expression. Loss of OsNAC5 function decreases Cd accumulation in rice grains. Our findings elucidate the transcriptional regulation of Cd stress response in rice and suggest biotechnological approaches to reduce Cd uptake in crops. Declaration of Competing InterestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

plant biology↗