Nature Communications

Bacterial biofilms underpin chronic infection and antimicrobial resistance, notably in Pseudomonas aeruginosa. Here we deconvolute a commercial alginate lyase preparation from Flavobacterium quisquiliarum and identify a previously uncharacterised ~21 kDa porphyrin-binding protein (FqPBP). Structural, biophysical and docking analyses reveal high-affinity tetrapyrrole binding. Recombinant FqPBP independently inhibits and disperses P. aeruginosa biofilms, implicating porphyrin sequestration and iron homeostasis in biofilm control and highlighting a potential therapeutic strategy targeting iron acquisition pathways.

Transient receptor potential (TRP) channels are evolutionarily conserved polymodal cation channels that mediate diverse sensory functions across the animal kingdom. Although TRP channels play key roles in peripheral sensation, their expression and functional relevance in the cerebral cortex remain poorly defined. Here, we integrate long- and short-read transcriptomics, targeted qPCR and membrane-aware proteomics to quantify TRP family members in adult mouse cortex. Across transcriptomic platforms, cortical TRP expression is dominated by TRPML, TRPC, and TRPM subfamilies, with lower representation of TRPP/TRPV, whereas Trpa1 and Trpv1 lie near empirical detection thresholds. Our proteomic workflow yields reproducible protein-level evidence for a subset of cortical TRPs, including TRPV2, TRPC4, TRPM3, TRPM7 and TRPP2, consistent with transcript rank order, while TRPA1/TRPV1 do not meet replicate-level protein-group detection criteria under 1% FDR control. Together, these multi-platform measurements establish a quantitative reference for cortical TRP biology and a framework for profiling low-abundance ion channels in complex brain tissue.

Endurance exercise imposes extreme metabolic demands on the adult human brain, raising the question of how core brain function is preserved under physiological challenge. We previously showed that marathon running induces reversible reductions in myelin within specific white-matter tracts, suggesting adaptive structural change under metabolic stress. Here, we asked whether this process is functionally tolerated. Neurophysiological recordings revealed maintained conduction latencies across motor, somatosensory, visual, and auditory pathways within 48 hours after race completion, indicating intact axonal signal transmission despite reduced myelin content. Cognitive testing revealed selective and transient modulation of higher-order processing, including attenuated practice-related gains in processing speed and short-lived increases in interference, whereas visuomotor speed and executive flexibility were preserved. All cognitive measures normalized one month after the race, supporting an adaptive framework linking myelin change with preserved brain function under extreme metabolic stress.

The QacA DHA2 exporter from Staphylococcus aureus is a prototypical multidrug transporter that, like other bacterial efflux pumps, can extrude a wide range of cytotoxic compounds thus playing a crucial role in antimicrobial resistance. Here, we report crystal structures of wild-type QacA in three key conformational states: inward-open, outward-open and ethidium-bound, representing the first ligand-bound structure of a 14 transmembrane helices (TM) DHA2 transporter. In combination with computational and functional studies, these structures provide a mechanistic framework to understand drug recognition and extrusion. Structural analyses reveal remarkable adaptability within the binding pocket, including a ligand-induced deformation of TM5 that enables coordination of ethidium bromide in the outward-open state. Molecular dynamics simulations show spontaneous lipid entry into the transporter core and suggest that substrate binding from the inner membrane leaflet initiates a conformational transition to an outward-open state, stabilizing high-affinity interactions. Subsequent binding site protonation drives substrate extrusion. Together, these findings elucidate the structural dynamics and mechanistic underpinnings of QacA-mediated multidrug transport, highlighting conformational flexibility and proton-coupled electrostatic changes as key determinants of multidrug recognition and extrusion. This study provides a foundational framework for developing targeted inhibitors to combat bacterial multidrug resistance.

Anaerobic carbon transformation in freshwater sediments drives substantial methane emissions globally, yet the microbial taxa linking complex carbon degradation to methane production remain poorly characterized. Here, we combined metagenomics with the first metatranscriptomic dataset from the anoxic sediments of meromictic Lake Cadagno (Swiss Alps) to identify the active microbial clades, metabolic pathways, and extrachromosomal elements (ecDNA) across a depth gradient within the upper 56 cm of sediment. We recovered 802 species-level metagenome-assembled genomes (MAGs) spanning 66 phyla and identified a Bacteroidota clade (VadinHA17) as one of the most abundant and transcriptionally active populations in the sediment. This clade encodes and transcribes a broad range of diverse glycoside hydrolases (GH), indicating a central role in complex carbohydrate degradation. Transcriptional profiles suggest that this clade ferments organic substrates to acetate and hydrogen, which are key substrates for methanogenesis. In line with this, the acetoclastic methanogen Methanothrix and hydrogenotrophic Methanoregula were among the most abundant and transcriptionally active archaea in the same depth layers. Beyond microbial genomes, we detected 86,905 viral OTUs (vOTUs) and 2,136 plasmid OTUs (pOTUs), with free viruses and plasmids accounting for 5-10% and 0.2% of all sequencing reads, respectively. Notably, plasmids and viruses associated with Bacteroidota VadinHA17 encode and transcribe GHs that could augment host carbohydrate-degrading capacity. Together, these findings reveal new details on how methane production in anoxic lake sediments emerges from a network spanning primary fermentation, methanogenesis and ecDNA-mediated metabolisms.

Shiga toxin-converting bacteriophages play a critical role in the emergence and virulence of pathogenic Escherichia coli strains. Despite their significance, detailed structural information on these phages remains scarce. Here we present a high-resolution cryo-electron microscopy and proteomic analysis of the phi24B bacteriophage, revealing an icosahedral capsid with T=9 symmetry, decorated by a processed esterase protein (gp84) and stabilized by cementing proteins. The tail assembly comprises a dodecameric portal, two rings of adapter proteins sharing a common fold, a hexameric nozzle, six lateral tail fibers, and a flexible central needle fiber. The binding sites of the fibers are described. Comparative analysis indicates conservation of the tail structure with related podoviruses but very different peripheral features.

More than 600 distinct skeletal muscles constitute up to 40% of the total mass of the human body. Human skeletal muscles differ in anatomical position, morphology, origin, and function, but the diversity of their molecular phenotypes, the gene expression and protein abundance profiles, remains poorly explored. Here, we report the large-scale CAGE-Seq promoterome profiling of 75 human skeletal muscles, complemented by 22 matched proteomes obtained with mass spectrometry. We identified 37001 transcribed regulatory elements and 1804 protein groups encompassing 1895 proteins, 80% of which demonstrated non-uniform expression across different muscles. The skeletal muscles of the eye, tongue, and diaphragm had the most distinctive molecular phenotypes, while the overall diversity was driven by hundreds of transcription factors with tissue-specific activity. By analyzing the allelic imbalance of CAGE-Seq reads, we discovered 6653 allele-specific single-nucleotide variants often coinciding with muscle-related GWAS SNPs, including muscle volume. Finally, we provide an interactive online atlas of transcriptomic and proteomic molecular phenotypes, facilitating further studies of gene regulation and heritable pathologies of skeletal muscles.

Understanding how natural and breeding selection interact to shape crop genomes is essential for improving resilience under climate change. Here, we applied a k-mer-based, alignment-free haplotype assignment approach to whole-genome resequencing data from 827 wheat landraces representing seven geographic groups and 208 modern cultivars. We identified haplotypes associated with local adaptation that were enriched in specific agroecological regions, many of which were derived from wild-relative introgressions. Comparative analyses revealed that natural and breeding selection largely targeted overlapping haplotype sets, but often drove them in opposite directions. Notably, haplotypes conferring adaptive advantages were frequently associated with negative regulation of agronomic traits, explaining their reduced prevalence among breeding-selected haplotypes. These results reveal the genomic basis of trade-offs between environmental adaptation and productivity and offer a framework for exploiting adaptive diversity in wheat improvement.

New antimalarial compounds are urgently required to overcome artemisinin partial resistance that has emerged in Asia and now Africa. Ozonides are promising next-generation artemisinins that offer the improved pharmacokinetic property of a prolonged in vivo half-life. To assess the potential for parasite resistance to ozonides in an artemisinin-resistant background, we subjected Cambodian Kelch13 (K13) mutant parasites to increasing artefenomel (OZ439) pressure up to in vivo physiological concentrations. Whole-genome sequencing identified a novel non-propeller K13 A212T mutation in OZ439-resistant parasites. Gene editing and drug susceptibility assays revealed that the K13 double mutation R539T+A212T is a determinant of OZ439 resistance. In extended parasite recovery assays, this resistance mechanism was associated with accelerated parasite recrudescence following OZ439 or OZ277 exposure. This phenotype was also observed in K13 C580Y+A212T double mutant parasites. Global metabolomic profiling revealed no changes in the levels of hemoglobin-derived peptides in OZ439-resistant parasites, suggesting that resistance is not associated with drug activation. Instead, double mutant parasites exhibited increased levels of metabolites linked to glutathione, nucleotide, and aspartate-glutamate metabolism, suggesting a higher capacity for redox regulation to tolerate drug-induced oxidative damage. Our findings demonstrate that ozonide resistance can emerge through a novel K13 mutation on the background of existing artemisinin-resistance k13 alleles.

Citrate is a central intermediate metabolite linking the tricarboxylic acid cycle and lipid biosynthesis. Tools for monitoring of spatiotemporal citrate dynamics are critical for getting a better understanding of cellular metabolism. Here, we develope genetically encoded excitation ratiometric biosensors for citrate, based on our previous intensiometric green fluorescence protein-based citrate biosensor, Citron1. We find that a single mutation in the Citron1 chromophore-forming tripeptide provided an excitation ratiometric response. Further rounds of directed evolution yield highly responsive variants, exhibiting citrate-dependent fluorescence changes between two excitation peaks. When expressed in mammalian cells, these biosensors enable citrate dynamics to be monitored in both the cytosol and mitochondria. Comparative analysis across multiple human breast cancer cell lines uncovers cell line-specific differences in citrate levels and their heterogeneity, which could be linked to their malignancy. Furthermore, flow cytometry-based measurements in mouse embryonic stem cells demonstrate the proteomics signatures underlying the population-level variability in citrate concentrations and citrate rewiring during stem cell differentiation. Together, these results show that these excitation ratiometric citrate biosensors enable quantitative, compartment-resolved, and population-scale analysis of cellular metabolism.

Sex-ratio distortion systems are promising genetic tools for mosquito population control. Two strategies have been proposed: prezygotic elimination of X-bearing sperm by X-shredding, which can drive invasive Y-chromosome transmission when sex distorters are Y-linked, and postzygotic daughter killing through disruption of X-linked haploinsufficient genes, a self-limiting approach known as X-poisoning. Previous attempts to implement X-poisoning in the malaria mosquito Anopheles gambiae unexpectedly produced prezygotic distortion, with sex bias arising from loss of X-bearing sperm rather than daughter lethality. Here we use a split CRISPR-Cas9 system to systematically compare sex-ratio distortion outcomes across germline Cas9 drivers and X-linked target genes. Meiotic X-chromosome targeting induced preferential Y-chromosome transmission regardless of target identity, function, or number of sgRNA target sites. In contrast, shifting Cas9 expression to earlier spermatogenic stages altered outcomes dramatically: targeting X-linked ribosomal protein genes caused severe developmental or reproductive toxicity, whereas targeting the haplolethal muscle gene wupA produced daughter-specific post-embryonic lethality, with the majority of surviving females emerging flightless. Tracking offspring using a Y-linked fluorescent marker confirmed that sex chromosome segregation remained unbiased, with female mortality accumulating progressively from the first larval instar, reaching near-complete lethality by adulthood. These results demonstrate that the timing of Cas9 expression during spermatogenesis, rather than target gene identity alone, determines the outcome of X-chromosome targeting in malaria mosquitoes, and establish the conditions required for genuine X-poisoning. Identification of wupA as an effective X-poisoning target provides a solid foundation for the future development of self-limiting Y-linked sex-ratio distortion systems for malaria vector control.

Isocitrate lyase 2 (ICL2) from Mycobacterium tuberculosis undergoes dramatic conformational rearrangements upon binding to the allosteric effector acetyl-CoA. Time-resolved cryo-EM captured conformational states along the ICL2 activation trajectory, revealing how acetyl-CoA binding at the allosteric sites leads to asymmetric, half-of-site activity at the catalytic centres. These findings support a conformational selection model of allostery, whereby acetyl-CoA binding shifts the pre-existing equilibrium towards an active state of the enzyme.

Wearable devices generate dense longitudinal heart rate (HR) data, but summarizing sustained heart rate elevation in a single daily metric remains challenging. We developed the heart rate persistence index (HRPI), defined as the largest integer k such that at least k minutes in a day have HR [≥] k bpm. For example, an HRPI of 105 means daily HR was [≥]105 bpm for at least 105 minutes. HRPI is threshold-free and integrates magnitude and duration of elevated HR into a single interpretable value. Using multi-day wearable recordings from a PhysioNet dataset, we show that HRPI captures structure beyond mean HR, reflects variability-related features, and exhibits robust day-to-day stability. In an independent healthy cohort, HRPI declines strongly with age, supporting physiological relevance. HRPI offers a compact, interpretable, and robust summary of sustained HR elevation for longitudinal wearable studies, providing information easily accessible to both specialists and nonspecialists.

Emerging infections and environmental disruptions increasingly threaten wildlife and ecosystem health. Free-ranging wildlife often serve as early indicators of ecological instability, making timely detection of morbidity and mortality events critical for early warning. Yet, existing systems lack the analytical capacity for real-time outbreak detection. We present WildAlert, an AI-driven early warning system that integrates fine-tuned BERT-based natural language processing models with unsupervised anomaly detection framework to identify unusual wildlife health events using real-time pre-diagnostic clinical data from wildlife rehabilitation organizations. The NLP module achieved high accuracy across clinical classifications and circumstances of admissions, enabling a pre-diagnostic syndromic surveillance framework. Retrospective validation demonstrated that WildAlert anomalies frequently coincided with or preceded confirmed morbidity events, including highly pathogenic avian influenza (HPAI), harmful algal bloom-associated toxicosis, cold-stunning in sea turtles, mass stranding events, West Nile virus, and mycoplasmosis. WildAlert establishes the worlds largest standardized, near real-time wildlife health surveillance system, transforming wildlife rehabilitation clinical records into actionable intelligence capable of detecting anomalies across taxa and regions, often before other surveillance methods. WildAlert provides a transferable analytical framework and scalable One Health model linking biodiversity monitoring, zoonotic disease preparedness, and ecosystem-linked environmental threats, with implications for conservation, public health and environmental hazard response.

NLRP3 is an innate immune sensor of a broad range of stimuli, which upon activation forms a multiprotein inflammasome complex triggering caspase-1 activation, IL-1{beta} and IL-18 maturation, and inflammatory cell death. The canonical NLRP3 activation pathway has been well characterized from a structural perspective. It involves the association of NLRP3 with membranes in the form of inactive oligomeric "cage" complexes, which, upon activation, convert to an active oligomeric NLRP3 disc. NLRP3 structural rearrangements during non-classical NLRP3 activation pathways, however, remain unknown. Here, we report a novel mode of NLRP3 activation utilized by the NLRP3 homolog from zebrafish. The cryo-EM structure of zebrafish NLRP3 shows that, unlike human NLRP3, it forms disc-shaped heptamers that undergo further trimerization, resulting in a 21-mer oligomeric arrangement. Surprisingly, a single zebrafish NLRP3 heptamer cannot arrange its PYD domains into a PYD helix and therefore requires a trimer of heptamers to form a PYD filament that enables ASC oligomerization. Furthermore, zebrafish NLRP3 does not associate with the Golgi network, nor does it form inactive "cage" oligomers or interact with NEK7. Thus, our data demonstrate an ancestral non-canonical structural mechanism of NLRP3 activation, which may shed light on alternative NLRP3 activation pathways present in humans.

Endosymbiosis of phytoplankton in heterotrophic hosts is ecologically important and has led to key evolutionary innovations. However, the dynamic molecular processes underlying endosymbiosis establishment remain poorly understood. Here, using large-particle sorting and liquid chromatography-tandem mass spectrometry, we unravel heterogeneous changes in proteomes of the cosmopolitan ciliate Paramecium and algal endosymbiont Chlorella from engulfment to stable endosymbiosis. The initial digestion sees a sharp decline of intracellular Chlorella cells, along with host cellular reorganization involving a reduction of the cortex-localized defensive organelles, trichocysts, and proteins for intracellular transport and recycling. The remaining Chlorella cells enter a bottleneck stage characterized by energy production and cell cycle commitment before active proliferation. Comparison of Paramecium with successful and failed endosymbiosis further identifies a solute carrier transporter that potentially mediates metabolic homeostasis of the endosymbiotic system. Our study reveals inter-organismal coordination during the transition from predator-prey to host-endosymbiont relationships. The approach of time-course single-cell dual proteomics can be useful for investigating diverse interactions between microbial eukaryotes.

Vegetative desiccation tolerance (VDT) has evolved independently across vascular plants, but its genetic basis remains poorly understood. Although VDT is associated with expansion of the ELIP gene family, the contribution of other lineage-specific expansions is unclear. We assembled genomes for Xerophyta elegans and Xerophyta humilis, identifying expanded gene families largely involved in chlorophyll metabolism and abscisic acid-mediated stress responses. Using a dense dehydration-rehydration transcriptome series in X. elegans seedlings, we reconstructed the regulatory network underlying VDT. Transcription factors from the ABF, ZAT and HSFC families were associated with early responses to desiccation. Key regulators of the seed maturation programme, including NAC transcription factors (ATAF1 and ANAC032), DOG genes and the trihelix factor ASIL1, were also implicated. These findings indicate that VDT arises through integration of abiotic stress signalling with rewiring of the seed maturation network, enabling desiccation tolerance in vegetative tissues.

Anaeramoeba pumila is a free-living anaerobic amoeba and the smallest known member of the Anaeramoebae, a phylum characterized by elaborate membrane-bound symbiosomes housing sulfate-reducing bacterial symbionts. Here, we report a draft nuclear genome assembly of A. pumila LANTAAN and describe the discovery, genomic characterization, and metabolic reconstruction of Candidatus Centrionella anaeramoebae gen. nov., sp. nov., an obligate intracellular symbiont of A. pumila belonging to the order Legionellales. Ca. Centrionella is a rare anaerobic member of Legionellales, a lineage otherwise comprising aerobic intracellular pathogens. Its genome (1.52 Mbp, 1,249 genes) is highly reduced and encodes an entirely anaerobic metabolism centered on substrate-level phosphorylation, arginine fermentation, and hydrogen oxidation via a bidirectional [NiFe]-hydrogenase -- metabolic strategies that parallel those independently evolved in the distantly related Anoxychlamydiales. The complete Dot/Icm type IVB secretion system is retained and likely mediates ongoing host manipulation, including via a large repertoire of predicted effector proteins. Strikingly, Ca. Centrionella has acquired eukaryotic Rac1-like GTPase genes from its host through horizontal gene transfer, with subsequent domain shuffling and duplication, that it may use to manipulate the cytoskeleton of its host. Unlike other Anaeramoeba symbionts, Centrionella localizes to the host microtubule-organizing center rather than a symbiosome, a localization consistent with cytoskeletal anchoring strategies described in other endosymbionts. The symbiosome, present in other Anaeramoeba species, appears to have been secondarily lost in A. pumila. A co-occurring Desulfobacter sp. LANTAAN, related to symbionts of other Anaeramoebidae, likely forms a tripartite syntrophic consortium by consuming hydrogenosomal fermentation end-products and supplying vitamin B12. Together, these findings illuminate the evolutionary transition in Legionellales from aerobic pathogenesis to anaerobic mutualism, providing a new model for the origins of intracellular symbiosis.

Adaptive embodied behavior involves transforming structured knowledge about the relationship between environment and action into motor signals, but how these transformations are coordinated across brain networks remain unknown. Participants learned associations between visual cues and isometric exertions that varied in force and duration, forming a two-dimensional cognitive map of a force-time space. During behavior, this force-time space was expressed in several cortical regions using grid-like coding schemes, indicating sensorimotor cognitive maps. Importantly, while mnemonic regions such as the entorhinal cortex maintained an unwarped, task-relevant representation, the primary motor cortex encoded a force-time space distorted by perceived effort during motor execution. Dynamic causal modeling showed inhibitory motor-to-mnemonic coupling that predicted the transformation of effort-weighted motor signals into sensorimotor maps. Furthermore, individual differences in learning and navigating the force-time space independently shaped mnemonic map geometry and perceived effort. These findings demonstrate that sensorimotor cognitive maps emerge from dynamic interactions between motor and mnemonic systems and are shaped by individual differences during the learning and execution of movement.

P2X receptors are trimeric ATP-gated ion channels that assemble as homo- or heterotrimers, with heteromeric forms exhibiting intrinsic asymmetry that influences function. Here, we report four high-resolution cryo-EM structures of human P2X2/3 heterotrimers representing distinct functional states, including ATP-bound assemblies (P2X332 and P2X223), the apo form, and a ligand/ATP-bound closed conformation. The three ATP-binding sites show asymmetric recognition of MgATP{superscript 2}- and ATP-, and channel activation requires occupancy of only two MgATP{superscript 2}- molecules. Gefapixant binds a single allosteric site and selectively inhibits MgATP{superscript 2}-, but not ATP-, binding, indicating orthosteric-allosteric coupling within the heterotrimer. Structural features of the transmembrane domain define ion permeation, particularly for Ca{superscript 2}. Despite asymmetric ligand interactions, gating remains largely symmetric, with minor differences in desensitization. These findings provide a structural framework linking asymmetry to coordinated channel function and open avenues for subtype-selective therapeutic intervention.