Biology subjects

Niu, X.

Publications and source records attributed to Niu, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Tumor γδ T-cell abundance is associated with favorable cancer treatment outcomes

Purpose: Clinical response to immune checkpoint blockade (ICB) remains variable. We asked whether immune-cell populations in the tumor microenvironment (TME) are associated with benefit across treatments and tumor types. Experimental Design: We analyzed pretreatment bulk tumor RNA-seq from ICB cohorts and TCGA. Gene-level effects associated with ICB response or TCGA survival were projected onto Human Primary Cell Atlas profiles of 157 cell types. Cox and mixed-effects models accounted for cancer type, cohort, and therapy, as appropriate. After {gamma}{delta} T cells emerged as a leading population, we adjusted their associations for eight CD8 estimators and evaluated them using TRUST4-based TRG/TRD reconstruction and single-cell RNA-seq. Results: {gamma}{delta} T-cell programs were among the signatures consistently associated with ICB response and favorable TCGA survival. Across ICB cohorts, {gamma}{delta} T-cell abundance was associated with response (n=1,356; OR, 1.38; 95% CI, 1.23-1.56) and overall survival (n=1,074; HR, 0.82; 95% CI, 0.76-0.88), with associations persisting after CD8 adjustment. ICB-response-associated cell-type profiles were strongly concordant with chemotherapy response (r=0.92) and moderately concordant with radiation response (r=0.58); targeted and hormone therapy analyses were underpowered. TRUST4 reconstruction and single-cell RNA-seq provided orthogonal support for the {gamma}{delta} signal. Conclusions: Pretreatment {gamma}{delta} T-cell abundance was associated with favorable ICB outcomes and survival across cancers, while related cell-type programs extended to selected non-immunotherapy response settings. Although associative and context dependent, these findings support prospective evaluation of {gamma}{delta} T-cell abundance as a candidate tumor-immune biomarker.

immunology↗

bioRxiv2026

Neural mechanisms of impaired self-compassion in depressed adolescents during social exclusion

Background: Self-compassion has shown to be an effective emotion regulation strategy, but its neural mechanisms remain understudied in adolescents with depression who suffer from social exclusion. This study employed event-related potentials to investigate the psychophysiological mechanisms underlying impaired self-compassion in adolescents with depression during social exclusion. Methods: Thirty-seven adolescents with major depressive disorder (age = 16.46 +/- 2.02) and thirty-two demographically matched healthy controls (age = 16.54 +/- 2.29) completed a social exclusion scenario imagination task. This task presented participants with social exclusion scenarios, asking them to imagine themselves as the excluded individual and subsequently rate their negative emotions. The regulation session required participants to use self-compassionate statements to regulate their emotional responses while imagining and rate how much self-compassion they have engaged in; the non-regulation required them not to use those statements and rate their negative emotions immediately following imagination. EEG signals were recorded during the task, and the late positive potential (LPP) was analyzed to examine the neural responses associated with self-compassion regulation following social exclusion. Results: Compared with the non-regulation condition, both groups showed less negative emotion during the self-compassion regulation condition. Adolescents with depression exhibited significantly lower self-compassion ratings than healthy controls, and showed a significantly smaller decrease in negative emotions. Higher self-compassion ratings were correlated with greater emotion regulation effect, particularly in adolescents with depression. Furthermore, LPP amplitudes were significantly higher in adolescents with depression than in healthy controls during both regulation and non-regulation conditions. Conclusions: Adolescents with depression were characterized by impairment in using self-compassion to downregulate negative emotions when confronted with social exclusion. LPP amplitudes were consistently elevated in adolescents with depression, underscoring their potential as a critical focus for psychophysiologically-informed therapies.

neuroscience↗

bioRxiv2026

Lack of ancestral SARS-CoV-2 imprinting promotes BA.3.2.2 infection in children

The ongoing evolution of SARS-CoV-2 is heavily constrained by population-level immune imprinting. Recent genomic surveillance reveals an unexpected demographic shift: the highly mutated BA.3.2.2 sublineage is significantly enriched in paediatric populations globally, unlike concurrent variants XFG and NB.1.8.1. Here, the evidence demonstrates that this paediatric susceptibility arises from the absence of ancestral Wuhan-strain immune imprinting. Serological analyses reveal a profound failure to neutralise BA.3.2.2 in young children with no ancestral strain exposure. Concurrently, single-B-cell sequencing analyses demonstrate that BA.3.2.2 completely evades Omicron-specific Class 1/4 neutralising antibodies, encoded by IGHV2-5 and IGHV5-51, which dominate the repertoires of weakly imprinted individuals such as young children. Conversely, BA.3.2.2 remains uniquely susceptible to broadly cross-reactive Class 1 antibodies, encoded by IGHV3-53/66, typically enriched in adults with strong ancestral imprinting, such as mRNA vaccine recipients. Critically, sustained transmission of BA.3.2.2 in paediatric populations may catalyse the emergence of secondary variants that combine the paediatric-evading features of BA.3.2.2 with adult-evading Class 1 mutations. This could allow the lineage to breach the imprinted immunity of the adult population, potentially driving widespread global transmission. Together, these findings show that legacy immune imprinting paradoxically provides superior protection against a highly divergent saltation variant, directly explaining the age-biased transmission of BA.3.2.2, and informing future paediatric vaccination strategies.

immunology↗

bioRxiv2026

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

Many fundamental mammalian brain functions emerge from the coordinated activity of cells distributed across large, brain-wide networks. To understand these processes in healthy and diseased states, ideally one would simultaneously measure and analyze single-cell activity at the brain-wide scale, an enduring challenge for live-measurement approaches that often face an inherent tradeoff between spatial resolution and scale. Here, we present GLOBE (sinGle-cell spatiotemporaL recOrding Brain-widE), a technology for brain-wide single-cell recording of cellular activity in vivo with spatiotemporal resolution, physiological sensitivity, and parallelization-accelerated readout. GLOBE leverages genetically encoded intracellular protein tape recorders and a high-throughput computational platform for integrated image and signal analysis. GLOBE records analog signal amplitudes across a continuous time axis, requires only standard light microscopy for in situ readout, and is compatible with expansion microscopy and RNA readouts. We applied GLOBE to simultaneously record transcriptional activity of the immediate early gene Fos in up to 219,703 neurons simultaneously across a single mouse brain over 5.5 continuous days, with a timestamp precision of 3.1-6.7 hours (median absolute error), a local recording density of 69-90% of neurons per imaging field of view, and a post-mortem imaging readout speed of 2.9 seconds per neuron on average. GLOBE resolves the brain-wide spatiotemporal structure of single-cell activity, revealing that Fos transcriptional dynamics associated with fear learning and memory retrieval are distributed across the brain with region-specific temporal heterogeneity, and that the variance of this structure scales down as the number of sampled cells increases. We envision GLOBE to have broad applications for dissecting and decoding physiological and pathological processes at the brain-wide scale.

neuroscience↗

bioRxiv2026

PalmaClust: A graph-fusion framework leveraging the Palma ratio for robust ultra-rare cell type detection in scRNA-seq data

MotivationSingle-cell RNA sequencing (scRNA-seq) is routinely used to build atlases of tissues, resolve developmental trajectories, and characterize disease microenvironments. Yet many biologically and clinically meaningful populations--including transient progenitors, therapy-resistant tumor subclones, and antigen-specific lymphocytes--occur at very low frequencies (<1%) and are easily missed by standard clustering pipelines. Existing approaches often require extensive manual curation, rely on known marker genes, or trade sensitivity for unacceptable false positive rates due to the insensitivity of metrics like the Gini index to heavy-tailed distributions. A scalable, statistically grounded method is needed to sensitively detect rare populations while providing calibrated confidence and interpretable molecular signatures. ResultsWe present PalmaClust, a graph-fusion clustering framework that repurposes Palma ratio--a tail-sensitive inequality metric in sociology--to identify marker genes driven by extreme sparsity. PalmaClust constructs and fuses multiple K-Nearest Neighbor (KNN) graphs derived from complementary gene-selection statistics including the Palma ratio, Gini index, and Fano factor. It employs a local refinement strategy that re-prioritizes Palma-ranked genes within parent clusters. Benchmarking across diverse public scRNA-seq datasets confirms that PalmaClust consistently outperforms state-of-the-art baselines, improving rare-class F1 scores by at least 20% (absolute) while maintaining high global clustering stability. Further studies demonstrate that the Palma ratio-derived graph layer is essential for capturing ultra-rare signatures that other views miss. Availabilityhttps://github.com/wan-mlab/PalmaClust.

bioinformatics↗

bioRxiv2026

Structure basis for single-strand nucleic acid targeting by IscB and variants

Transposon-encoded IscB has been established as the evolutionary ancestor of CRISPR-Cas9. This compact RNA-guided endonuclease has since been engineered for genome editing applications. We previously repurposed IscB and Cas9 as efficient RNA editors by removing their double-stranded DNA recognition module, the TAM/PAM-interacting domain. Here, we report four cryo-EM structures of IscB in complex with single-stranded nucleic acid (ssNA) targets to illuminate its mechanistic underpinnings. Structural analysis reveals that IscB initially facilitates formation of a 10-nt seed duplex with ssNA; however, further base-pairing is blocked by an alternatively positioned HNH nuclease that acts as a conformational roadblock. In this intermediate state, neither HNH nor RuvC is competent for target cleavage: the HNH domain is occluded by the roadblock configuration, while the RuvC active site is obstructed by the guide RNA. Only upon full duplex formation do additional base pairs between the guide RNA and ssNA dislodge the HNH roadblock, simultaneously exposing the RuvC nuclease active site. We propose that an analogous conformational checkpoint governs IscB activity during dsDNA target interrogation. Guided by these structural insights, we introduced mutations to either enhance ssNA binding or relieve the conformational checkpoint, both of which significantly improved RNA-targeting efficiency of IscB.

biochemistry↗

bioRxiv2026

Proteolytic processing of Argonautes in multiphase condensates promotes transgenerational epigenetic inheritance

Epigenetic information can be memorized in perinuclear condenates to transmit across generations to modulate gene expression in descenent. Here, we identify a conserved N terminal proteolytic mechanism in Caenorhabditis elegans that is essential for small RNA-mediated transgenerational epigenetic inheritance (TEI) and for maintaining germline immortality. Two conserved, perinuclear germ granule subcompartments-enriched N-terminal processing peptidases, APP-1 and DPF-3, act cooperatively to trim N-terminal intrinsically disordered regions of the Argonaute proteins WAGO-1, WAGO-3, and WAGO-4. This processing shields these Argonautes from proteasome-mediated protein degradation, prevents the loss of their associated small RNAs, and promotes their accumulation in germ granules subcompartments. In contrast, unprocessed WAGOs are recognized and destabilized by the conserved E3 ubiquitin ligases RNF-1 and UBR-7. We propose that this cooperative proteolytic mechanism adds another layer of sspatiotemporal regulation over small RNA-directed epigenetic inheritance and may represents a broadly conserved strategy for regulating protein homeostasis and gene expression programs.

cell biology↗

bioRxiv2025

IGHV3-53 antibody abundance drives divergent SARS-CoV-2 immune imprinting

The mechanisms driving divergent SARS-CoV-2 immune imprinting in populations with distinct SARS-CoV-2 exposure histories remain unclear. However, conventional wild-type mouse models fail to recapitulate severe imprinting, even after potent ancestral-strain mRNA immunization, hindering imprinting-related mechanistic investigation and vaccine evaluation. Here, we surprisingly found that V(D)J-humanized mice could faithfully recapitulate human severe imprinting phenotypes. Comprehensive antibody repertoire analysis and deep mutational scanning-based epitope mapping of 583 monoclonal antibodies from these models revealed that the pre-existing IGHV3-53/66 antibody abundance determine imprinting severity through antibody-mediated masking of Omicron-specific epitopes. Both passive IGHV3-53/66 antibody transfer and IGHV3-53 knock-in were sufficient to induce severe imprinting in wild-type mice. Together, these findings demonstrate that the V(D)J germline repertoire--even a single germline-encoded antibody response--can profoundly shape humoral imprinting severity. Accordingly, we established an IGHV3-53 knock-in mouse model that accurately recapitulates the human antibody landscape, providing a valuable tool for guiding future COVID-19 vaccine updates.

immunology↗

bioRxiv2025

JNK integrates immune and stress signals to balance apoptosis and proliferation in airway progenitors

Chronic inflammation disrupts epithelial regeneration, yet how immune signaling reprograms progenitor fate remains unclear. Using the Drosophila airway as a model of epithelial remodeling, we identify the c-Jun N-terminal kinase (JNK) pathway as a central integrator of immune and stress cues that balances apoptosis and compensatory proliferation in airway progenitors. Persistent activation of the innate immune IMD pathway induces simultaneous cell death and proliferation through a non-canonical route that bypasses NF-{kappa}B/Relish and instead engages JNK. Downstream, distinct transcriptional modules orchestrate these divergent fates: Foxo and AP-1 drive apoptosis, whereas the ETS factor Ets21C mediates proliferation. Genetic inhibition of JNK or its effectors restores progenitor homeostasis, while constitutive activation recapitulates inflammation-induced tissue remodeling. These responses are cell-autonomous, revealing that airway progenitors actively interpret immune and stress signals to determine their fate. Collectively, our findings uncover a modular signaling architecture that links inflammation to regeneration and highlight conserved JNK-dependent transcriptional programs as potential therapeutic targets to prevent progenitor exhaustion in chronic airway disease.

cell biology↗

bioRxiv2025

Genetic diversity in horseshoe bat ACE2 and sarbecovirus spike proteins mutually shape one another

Angiotensin-converting enzyme 2 (ACE2) serves as the entry receptor for a wide diversity of sarbecoviruses naturally harboured by horseshoe bats (genus Rhinolophus). Despite the extensive circulation of these viruses in many horseshoe bat species, the potential interactions between virus and receptor evolution remain poorly understood. We sampled individuals of the intermediate horseshoe bat (Rhinolophus affinis) across Vietnam and identified 15 genotypes of ACE2 proteins, 10 of which are previously unreported. Phylogenetic analysis and infectivity assays with a panel of 36 sarbecovirus spike proteins indicated that the R. affinis ACE2 phylogeny has geographic structuring and genotypes originating from different geographic regions exhibit distinct infectivity phenotypes. We detected site-specific positive selection on ACE2 site 24 with the associated substitutions largely affecting the receptors sarbecovirus infectivity profile. Together, our findings suggest that the R. affinis within-species ACE2 diversity has likely been shaped through selection by past sarbecovirus infection. Similarly on the virus end, we use mutagenesis assays and structural analysis through cryo-EM, to delineate the proximal evolution of the Ra22QT77 spike defined by specialization to the ACE2 genotypes of horseshoe bats found in and near southern Vietnam, where the virus was sampled. Our findings contribute to a better understanding of host-sarbecovirus co-evolution dynamics and provide valuable insights into the receptor usage determinants of these viruses. HighlightsO_LIWe identify a total of 15 ACE2 genotypes in R. affinis bats from Vietnam. C_LIO_LIACE2 intraspecific polymorphism is geographically separated and associated with distinct sarbecovirus infectivity. C_LIO_LISite 24 of R. affinis ACE2 experiences positive selection and controls susceptibility to sarbecoviruses. C_LIO_LIBat ACE2s and sarbecovirus spikes are bidirectionally shaped by each others evolution. C_LI

microbiology↗

bioRxiv2025

A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging

Recent advances in high throughput optical microscopy have achieved whole-organism scale imaging at diffraction-limited resolutions. Current microscopes, however, require making compromises between achieving the optimal resolution, imaging depth, multispectral capability, and data throughput due to limitations in optical design and data stream handling. We have created a parallel-line scanning confocal microscope (plSCM) which provides 1.1 Gigavoxels/second high speed imaging while achieving an optical resolution of [~]180 x 220 x 650 nm with 2 millimeters of imaging depth in 3 simultaneous spectral channels. To handle such a massive imaging data stream, we have engineered a scalable network-distributed image acquisition/processing framework (SNDiF), which allows continuous capture, real-time processing, and cluster storage of petabyte-scale single image datasets in days. Together, our parallelly distributed microscope and software system presents a general solution for large-scale high-throughput and high-resolution multicolor imaging which can operate for days at a time.

bioengineering↗

bioRxiv2025

JAK/STAT Signaling Governs Airway Epithelial Homeostasis and Stress Resilience in Drosophila

Airway epithelia must maintain barrier integrity while continuously adapting to changing environmental conditions. This requires key signaling pathways in airway epithelia to operate within a tightly controlled functional range. Here, we show that airway epithelial homeostasis in Drosophila depends on balanced JAK/STAT signaling. Basal pathway activity is constitutively present in differentiated epithelial cells and is necessary for cell survival, epithelial integrity and stress resistance. In accordance with this role as a stress responsive regulator in epithelial biology, environmental stressors, including hypoxia, cigarette smoke, and cold exposure, induce JAK/STAT signaling. In contrast, sustained pathway activation is associated with airway remodeling characterized by epithelial thickening, luminal narrowing, and altered cellular organization. Transcriptomic analysis reveals that sustained activation is associated with a coordinated epithelial stress program integrating immune signaling, proteostasis, and metabolic adaptation. Cross-species comparisons with murine and human datasets suggest that key aspects of this response are conserved. Pharmacological inhibition demonstrates that remodeling depends on continued pathway activity and can be partially reversed in vivo. Together, our findings support a model in which airway epithelial homeostasis depends on maintaining JAK/STAT signaling within a defined functional range. This "Goldilocks" principle provides a conceptual framework for understanding how epithelial stress responses are balanced under physiological and pathological conditions. Graphical abstract

cell biology↗

bioRxiv2025

Forest biogeochemical monitoring indicates altered microbial communities, macronutrient availability, CO2 emissions and litter chemistry in root zone soil of oak trees with Acute Decline symptoms

Acute and Chronic Oak Decline (AOD & COD) widely impact oak woodlands across Europe. AOD is known to cause rapid decline in tree health in a short span of 3-5 years. However, the interactions between such oak decline and soil biogeochemical dynamics are not fully understood. We selected three oak trees for each of the three treatments for biogeochemical monitoring: 1. No symptoms (Healthy), 2. AOD & 3. COD symptoms, in Writtle woodlands, Essex, UK. The selected trees were used for quarterly root zone soil sampling (cores to depth of 40 cm), and monthly surface soil (0-10 cm), leaf litter and GHG emissions sampling over a year (2022-23). Soil samples were characterised for their physico-chemical properties, total nutrient content & availability. Leaf litter samples were sorted into branches, leaves, seeds and flowers, weighed and their chemistry characterised. Soil microbial communities were characterised using phospholipid fatty acid analyses. Almost all the measured properties showed significant changes with season and depth, indicating a strong temporal and depth effect on forest soil biogeochemical dynamics. Notably macro-nutrient contents of leaf litter were greater in the summer period, which resulted in increased soil nutrient availability in autumn. This pattern was particularly exaggerated in AOD trees, which had greater nutrient content in litterfall in summer and greater nutrient availability in root zone soil in autumn than those of COD and Healthy trees. We found that AOD root zone soil have altered microbial communities, decreased CO2 emissions and increased macronutrient availability. Taken together, our study shows poor physiological nutrient management by diseased AOD trees revealed by greater nutrient concentration in AOD leaf litter indicating the lack of nutrient resorption and re-allocation before leaf senescence, and less active root zone soil under AOD trees, shown by reduced soil CO2 emissions and increased nutrient availability in oak root influenced zones. Hence, we conclude that the biogeochemical dynamics of AOD root zone soils are significantly different to that of healthy and COD trees, however controlled experiments are needed alongside these field observations to disentangle the causes from effects in understanding the relationship between soil health and oak decline. HighlightsO_LIWe monitored forest soil biogeochemical dynamics under oak trees of different health status C_LIO_LIAcute Oak Decline (AOD) trees had greater macronutrient availability in root zone soils C_LIO_LIAOD trees had greater nutrient content in litter added to the root zone soil C_LIO_LIAOD root zone soils had altered microbial community structure & reduced CO2 emissions C_LIO_LIWe conclude that AOD trees have poor physiological nutrient management and less active rhizosphere compared to healthy trees. C_LI

ecology↗

bioRxiv2025

Manifold Transform by Recurrent Cortical Circuit EnhancesRobust Encoding of Familiar Stimuli

A ubiquitous phenomenon observed along the ventral stream of the primate hierarchical visual system is the suppression of neural responses to familiar stimuli at the population level. The observation of the suppression of the neural response in the early visual cortex (V1 and V2) to familiar stimuli of size that are multiple times larger in size than the receptive fields of individual neurons reflects the plausible development of recurrent circuits for encoding these global stimuli. In this work, we investigated the neural mechanisms of familiarity suppression and showed that an excitatory recurrent neural circuit, consisting of neurons with small and local receptive fields, can develop to encode specific global familiar stimuli robustly as a result of familiarity training. This Hebbian learning based model attributes the observed familiarity suppression effect to the sparsification of the population neural code for the familiar stimuli due to the formation of image-specific local excitatory circuits and competitive normalization among neurons, leading to the paradoxical neural response suppression to the familiar stimuli at the population level. We explored the computational implications of the proposed circuit by relating it to the sparse manifold transform. The recurrent circuit, by linking spatially co-occurring visual features together, compresses the dimensions of irrelevant variations of a familiar image in the neural response manifold relative to the dimensions for discriminating different familiar stimuli. The computation can be considered as a globally non-linear but locally linear manifold transform that orthogonalizes the slow modes of network dynamics relative to the subspace of irrelevant stimulus variations, resulting in increased robustness of the global stimulus representation against noises and other irrelevant perturbations. These results provide testable predictions for neurophysiological experiments. Author summaryIn this research, we explored how the brain can become more efficient at processing familiar visual information. When we repeatedly see something, our brains response to it changes. In response to familiar stimuli, neurons across the different visual areas of the mammalian visual system become more selective and their overall activities decrease. We developed a computational model to investigate why this happens and what functional advantages these mechanisms might provide. We discovered that familiarity leads to the development of a more efficient and robust neural representation of what we see. It allows us to rapidly and robustly recognize our friends face despite changes in lighting conditions, view angle, or facial expression. Our model showed that through repeated exposure, the brains neural circuits, even in the early stages of visual processing, rapidly adapt and organize themselves to focus on important and consistent features in our visual environment while becoming less sensitive to irrelevant variations, and distractions.

neuroscience↗

bioRxiv2024

Nematode-Trapping Fungus Arthrobotrys oligospora is Hungry for COQ7 to Alleviate Environmentally Triggered Iron Overload

Choosing the right and appropriate amount of substances in a changing environment is essential for the growth and survival of all species. We found that elevated oxygen levels significantly enhanced the iron-rich trapping devices of a nematode-trapping fungus (NTF), Arthrobotrys oligospora. Interestingly, genomic analysis revealed that all NTFs lacked coq7, a key gene involved in ubiquinol (UQ) biosynthesis and iron chelation. Notably, A. oligospora utilizes UQ instead of UQ for low-aerobic respiration. Transcriptional, metabolic, mutational, and phenotypic analyses revealed that A. oligospora produces a chemotaxonomic class of highly oxygenated arthrobotrins with characteristics similar to UQ skeleton, for high-aerobic respiration. Disruption of arthrobotrin biosynthesis in the {Delta}art mutant not only enhanced UQ biosynthesis, but also triggered trapping device formation and nematicidal activity under elevated oxygen conditions. The addition of UQ to both wild-type and {Delta}art mutants strongly inhibited trapping device development. Remarkably, the iron-rich trapping devices preferentially capture N2 nematodes harboring iron-chelating COQ7 with ferritin properties. Time-calibrated evolutionary analyses, combined with geological data, indicated that the NTF ancestor lost the coq7 gene after acquiring the arthrobotrin biosynthetic gene cluster during the "superoligotrophy" period, characterized by dramatic shifts in global oxygen levels and temperature changes. Our results demonstrate that oxygen is a critical factor in inducing iron overload, highlighting the origin and role of coq7 loss in the evolution of predatory behavior of NTFs. Our finding that NTFs capture nematodes for iron chelation therapy, rather than for food, explains a long standing debate about the limited carnivorous ability of trapping devices.

microbiology↗

bioRxiv2024

A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments

High-throughput microscopy necessitates 3D image storage, visualization, and analysis in terabyte to petabyte scales. Centralized high-performance computing (HPC) infrastructure provides the resources, but interfacing software is limited. We developed an extensible platform with a scalable image storage format (SISF) and content delivery network (CDN) to enable fast, random access to compressed data. Additionally, we built a cloud-based nTracer2 software to annotate neuron morphology from SISF images in a web browser.

bioinformatics↗

bioRxiv2024

Thermophilic Fungus Uses Anthraquinones to Modulate Ferrous Excretion, Sterol-Mediated Endocytosis and Iron Storage in Response to Cold Stress

To date, there is no real physiological mechanisms for iron excretion in eukaryote, and no physiological "actuator" that can control all the three fundamental biologic processes of absorption, storage and excretion. Here we observed that the accumulation of anthraquinones by Thermomyces dupontii under cold stress can achieve this process. Through mutation analysis, we found that mutant {Delta}An deficiency in anthraquinones accumulated ferrous and total free iron due to adopting a rare lifestyle with no endocytosis but accumulation of membrane-derived vesicles. Anthraquinone complement indicated that the vesicles in {Delta}An could coat the extrinsic anthraquinone-induced granules to prevent contact with the fungal interiors. Detailed chemical investigation on {Delta}An led to characterization of a rare oxygen-free ergosterene with unstable nature in air as the major membrane steroid in {Delta}An, suggesting hypoxia inner in {Delta}An cells, consistent with dramatically low oxygen-consuming rates in {Delta}An. A series of physiological and metabolic analysis indicated anthraquinones were involved in exporting ferrous and promoting formation of oxygen-containing metabolites, including ergosterols for endocytosis and iron chelators for iron storage. Moreover, we found that both the anticancer agent mitoxantrone with well know-cardiotoxicity side effect and the major terpenoid-derived polycyclic aromatics from Danshen for treating cardiovascular disease showed potent ferrous transporting capabilities in human cancer cells. Our findings provide a novel insight into the underlying mechanisms of polycyclic aromatics in nature and pharmacology, and offer new strategy for developing potential therapeutics and agents for membrane transport, iron homestasis and anticold. Graphical AbstractUp to now, regulation of iron homeostasis by metabolites have rarely been characterized. Moreover, no excretory mechanisms for iron in fungi have been reported. In this study, we found that Thermomyces dupontii can accumulate a large amount of anthraquinones under cold stress. The anthraquinones can release free ferric ion, reduce ferric to ferrous ions, and export ferrous ions, greatly enhancing thermophilic fungus to survive in the bio-system environment. Furthermore, lack of the anthraquinones can inhibit oxygen-dependent ergosterol mediated endocytosis, leading to an self-imposed isolation via oxygen-free ergosterene-mediated cell membranes. Importantly, the well known anthraquinone compound Mitoxantraquinone for anticancer and the main terpenoid polycyclic aromatic metabolites in traditional Chinese medicine Danshen for the treatment of cardiovascular diseases both exhibit strong ferrous ions transport capabilities. Our findings provided new insights for developing potential therapies and drugs for iron homeostasis and drug delivery. O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/605589v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@114551eorg.highwire.dtl.DTLVardef@1e03589org.highwire.dtl.DTLVardef@dad51borg.highwire.dtl.DTLVardef@dd0601_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Harnessing in vivo Synthesis of Bioactive Multiarylmethanes in Escherichia coli via Oxygen-Mediated Free Radical Reaction Induced by Simple Phenols

BackgroundXanthenes and multi-aryl carbon core containing compounds represent different types of complex and condensed architectures that have impressive wide range of pharmacological, industrial and synthetic applications. Moreover, indoles as building blocks were only found in naturally occurring metabolites with di-aryl carbon cores and in chemically synthesized tri-aryl carbon core containing compounds. Up to date, rare xanthenes with indole bearing multicaryl carbon core have been reported in natural or synthetic products. The underlying mechanism of fluores-cein-like arthrocolins with tetra-arylmethyl core were synthesized in an engineered Escherichia coli fed with toluquinol remained unclear. ResultsIn this study, the Keio collection of single gene knockout strains of 3901 mutants of E. coli BW25113, together with 14 distinct E. coli strains, was applied to explore the origins of endoge-nous building blocks and the biogenesis for arthrocolin assemblage. Deficiency in bacterial res-piratory and aromatic compound degradation genes ubiX, cydB, sucA and ssuE inhibited the mu-tant growth fed with toluquinol. Metabolomics of the cultures of 3897 mutants revealed that only disruption of tnaA involving in transforming tryptophan to indole, resulted in absence of arthro-colins. Further media optimization, thermal cell killing and cell free analysis indicated that a non-enzyme reaction was involved in the arthrocolin biosynthesis in E. coli. Evaluation of redox potentials and free radicals suggested that an oxygen-mediated free radical reaction was respon-sible for arthrocolins formation in E. coli. Regulation of oxygen combined with distinct phenol derivatives as inducer, 31 arylmethyl core containing metabolites including 13 new and 8 biolog-ical active, were isolated and characterized. Among them, novel arthrocolins with p-hydroxylbenzene ring from tyrosine were achieved through large scale of aerobic fermentation and elucidated x-ray diffraction analysis. Moreover, most of the known compounds in this study were for the first time synthesized in a microbe instead of chemical synthesis. Through feeding the rat with toluquinol after colonizing the intestines of rat with E. coli, arthrocolins also ap-peared in the rat blood. ConclusionOur findings provide a mechanistic insight into in vivo synthesis of complex and condensed ar-throcolins induced by simple phenols and exploits a quinol based method to generate endoge-nous aromatic building blocks, as well as a methylidene unit, for the bacteria-facilitated synthesis of multiarylmethanes.

biochemistry↗