The growing threat of antimicrobial resistance (AMR) necessitates the rapid discovery of novel antimicrobial peptides (AMPs) as alternative therapeutics. However, most computational approaches rely on binary AMP or non-AMP classification or permissive MIC thresholds (e.g. ≤128 μg/mL), offering limited biological interpretability and translational value. We present CVAE-BIO, a biochemical-knowledge-driven, multi-module pipeline for the discovery of AMPs targeting drug-resistant E. coli as a model pathogen yet generalizable to other bacterial targets. The model integrates a conditional variational autoencoder (CVAE) constrained by key biochemical properties (MIC≤10 μg/mL, net charge > + 2, peptide length < 40 residues, instability index <40, and Boman index <0) with a Random Forest classifier trained on 30 biochemical descriptors. In vitro validation showed that 18.5% of generated peptides exhibited strong activity (MIC≤10 μg/mL), with 38.9% reaching MIC ≤50 μg/mL while maintaining key biochemical properties. Most validated novel peptides are narrow-spectrum AMP targeting E. coli. Wet-lab results also showed that highly active cationic-amphipathic AMPs are characterized by significantly low counts of tiny and small residues, suggesting that avoiding using these residues or limiting them to a maximum of 2 and 3, respectively, might improve the activity of AMP. Taking both antimicrobial activity and hemolytic toxicity into account, 9 peptides were identified as non-toxic and active AMP candidates. This explainable framework enables efficient AMP discovery under biochemical constraints and yields experimentally validated candidates with translational potential.

Biological nitrogen fixation is a cornerstone of terrestrial nitrogen cycling, traditionally attributed to bacterial nitrogenase activity. However, the potential contribution of rhizospheric viruses remains largely unexplored. Here, we reveal the global distribution of nitrogen-fixing genes, with widespread detection of nifA, nifL, nifU, and nifH in both bacteria and viruses, and identify nifU as a viral auxiliary metabolic gene (AMG). Analysis of viral communities in rhizosphere and bulk soils cultivated with cowpea showed that viral nifU expression was significantly upregulated in rhizosphere soils. Using 15N₂ stable-isotope tracing and virus transplantation experiments, we demonstrate that virus-encoded nitrogen-fixing AMGs, horizontally transferred from bacteria such as Azospirillum thermophilum (70–99% homology), increased nitrogenase activity from 1.79 to 3.14 nmol C2H4 g-1 dry soil h-1. This enhancement was accompanied by shifts in bacterial community composition, with the relative abundance of the nitrogen-fixing genus Azotobacter reaching 90.8%. These results uncover a previously hidden role of rhizospheric viruses in promoting bacterial nitrogen fixation, suggesting that viral-mediated gene transfer could be leveraged to enhance nitrogen cycling in soils and inform sustainable soil management strategies. Biological nitrogen fixation is crucial for soil fertility and is often attributed to bacteria. This study reveals that viruses can facilitate bacterial nitrogen fixation by encoding the auxiliary metabolic gene nifU.

Despite advances in mass spectrometry and emerging single-molecule approaches, sequencing peptides at the single-molecule level remains a central challenge in proteomics. Here we present a ‘reverse translation’ strategy that enables single-molecule peptide sequencing with single-amino-acid resolution. In this approach, peptides undergo a modified Edman degradation that iteratively releases N-terminal amino acids tagged with peptide-specific DNA barcodes. Antibody-mediated proximity extension assays identify these barcoded amino acids and generate PCR-amplifiable DNA reporters that record the identity, position and originating peptide of each amino acid. The resulting DNA library is directly read by high-throughput sequencing, converting peptide sequences into digital DNA outputs. Using this approach, we demonstrate true single-molecule peptide sequencing, achieving full sequence coverage in millions of reads and accurate differentiation of both native and post-translationally modified peptides. These results establish a framework that redefines protein sequencing as a DNA sequencing problem and lays the foundation for high-throughput, de novo single-molecule protein sequencing. Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.

The mushroom innovation ecosystem highlights significant advances in mycology, biotechnology, and biofabrication, as well as the role of startups in translating these breakthroughs into products. By tracing these translational pathways, this Perspective aims to demonstrate that mushrooms represent more than a scientific resource - they embody a cross-sectoral model for bioinspired innovation with profound impact on sustainable industry and human wellbeing. This Review article explores how startups translate advances in mycology, biotechnology and biofabrication to address pressing environmental and societal challenges. It positions mushrooms as a cross-sector platform for sustainable innovation with wide-reaching benefits for industry and human wellbeing.

Tumor immunotherapy is often compromised by an immunosuppressive tumor microenvironment (TME) characterized by abnormal vasculature and exhausted T cells. Here, given the role of nitric oxide (NO) in favorably remodeling the TME, we engineered Escherichia coli Nissle 1917 (ECN) with a synthetic arginine–NO circuit (ECN-NO) that modifies the arginine synthesis pathway to constitutively synthesize arginine and enable sustained NO production. Specifically, deletion of the arginine repressor ArgR relieved feedback inhibition of arginine biosynthesis, whereas co-expression of argininosuccinate synthase and lyase (ArgG/ArgH), together with Bacillus subtilis nitric oxide synthase (BsNOS), enabled sustained NO production through enhanced arginine regeneration. Intratumoral colonization of ECN-NO significantly enhanced the antitumor efficacy of anti-programmed cell death ligand 1 (αPD-L1) immunotherapy, resulting in durable tumor regression across multiple solid tumor mouse models. Mechanistically, ECN-NO induced vascular normalization and dendritic cell recruitment, alleviated tumor immunosuppression and synergized with αPD-L1 to expand functional CD8+ T cells, reverse T cell exhaustion and promote memory T cell formation, establishing antitumor immunity for at least 120 days. Solid tumors are sensitized to anti‑PD‑L1 immunotherapy by engineered E. coli to produce nitric oxide.

Alternative splicing (AS) has emerged as a regulatory layer in plant adaptation to the environment. In particular, biotic stresses trigger a drastic remodeling of the plant AS landscape, with minimal overlap with changes at the gene expression level, suggesting an additional, albeit poorly understood, mechanism of regulation. Recent studies have revealed that effectors from unrelated pathogens target core spliceosome components as well as accessory splicing factors. While this targeting is beginning to shed light on the relevance of the modulation of the plant AS landscape for pathogen invasion, it has also led to the identification of novel splicing factors, allowing the discovery of unexplored characteristics of the plant splicing machinery. Here, we review this emerging field, which delineates an additional battleground in the evolutionary arms race between plants and pathogens and has the potential to advance our biochemical and mechanistic understanding of the plant spliceosomal complex.

Chemical innovation is essential for fungi to adapt to ever-changing ecological environments. However, the environmental and evolutionary drivers of fungal metabolic differentiation remain ambiguous. Here, we show the phylogeographic diversity of 1052 Aspergillus flavus strains across four continents, as conducted through phylogenetic and biogeographical analysis, including 544 newly sequenced strains from China. These strains exhibit varying levels of population-specific mycotoxin production, as determined by population metabolomics analysis. We report a toxigenic subpopulation from China, identified through comparative population genomics analysis. Pan-metabolome analysis reveals strong phylogeographic metabolic patterns associated with specific ecological niches. Low-mycotoxin production clades harbor distinct uncharacterized biosynthetic gene clusters and produce different specialized metabolites instead. This discrepancy is only partially explained by variation in biosynthetic pathway genes, and changes in regulation and primary metabolism appear to mainly drive differentiation of specialized metabolite profiles across fungal populations, as indicated by pangenome profiling, metabolites-genome-wide association study, genotype-environment association study, pan-transcriptome analysis, and gene knockout experiments. Altogether, our results reveal how environmental shifts drive the fungal metabolic evolution, and provide insights for predicting the risk of harmful fungal outbreaks and for biogeographically-informed, precise control measures. Drivers of fungal metabolic diversity are incompletely understood. Here, the authors conduct a global genomics study of over 1,000 pathogenic fungi to show that geography shapes the metabolic diversity in Aspergillus flavus revealing how climate drives fungal chemical adaptive evolution.

Asgard archaea were pivotal in the origin of complex cellular life. Heimdallarchaeia (a class within the phylum Asgardarchaeota) are inferred to be the closest relatives of eukaryotes. Limited sampling of these archaea constrains our understanding of their ecology and evolution, including their role in eukaryogenesis. Here we use massive DNA sequencing of marine sediments to obtain 404 Asgardarchaeota metagenome-assembled genomes, including 136 new Heimdallarchaeia and several novel lineages. Analyses of their global distribution revealed they are widespread in marine environments, and many are enriched in variably oxygenated coastal sediments. Detailed metabolic reconstructions and structural predictions suggest that Heimdallarchaeia form metabolic guilds that are distinct from other Asgardarchaeota. These archaea encode hallmark proteins of an aerobic lifestyle, including electron transport chain complex (IV), haem biosynthesis and reactive oxygen species detoxification. Heimdallarchaeia also encode novel clades of respiratory membrane-bound hydrogenases with additional Complex I-like subunits, which potentially increase proton-motive force generation and ATP synthesis. Thus, we propose an updated Heimdallarchaeia-centric model of eukaryogenesis in which hydrogen production and aerobic respiration may have been present in the Asgard-eukaryotic ancestor. This expanded catalogue of Asgard archaeal genomic diversity suggests that bioenergetic factors influenced eukaryogenesis and constitutes a valuable resource for investigations into the origins and evolution of cellular complexity. Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgardarchaeota, in conditions that may have given rise to early eukaryotes.

Recent advances in genetic engineering have provided diverse tools for artificially diversifying both prokaryotic and eukaryotic cell populations. However, achieving precise control over the ratios of multiple cell types within a population derived from a single founder remains a major challenge. Here we introduce a suite of recombinase-mediated genetic devices designed to accurately control population ratios, enabling the distribution of distinct functionalities across multiple cell types. We systematically evaluated key parameters that influence recombination efficiency and developed data-driven models to reliably predict binary differentiation outcomes. Using these devices, we constructed parallel and series circuit topologies to implement user-defined, multistep cell-fate branching programs. The branching devices facilitated the autonomous differentiation of precision fermentation consortia from a single founder yeast strain, optimizing cell-type ratios for applications such as pigmentation and cellulose degradation. Similar effects were obtained with mammalian cells. We also engineered multicellular aggregates with genetically encoded morphologies by coordinating self-organization through cell adhesion molecules. Our work provides a comprehensive characterization of recombinase-based cell-fate branching mechanisms and introduces an approach for constructing synthetic consortia and multicellular assemblies. A synthetic genetic circuit made up of recombinase-based cell-fate branching devices enables precise control over the ratios of cell types in an offspring population derived from one founder strain, and could be used to build user-defined multicellular aggregates.

Photosensory protein domains, derived from nature, are foundational for optogenetic protein engineering. Tailoring their properties enables their full exploitation for optogenetic regulation in basic research and applied bioengineering applications. Here, we present a simple, yet powerful strategy based on random mutagenesis coupled to high-throughput screening that allowed altering the most fundamental properties of the widely used nMag/pMag photodimerization system: its light sensitivity and activation. Variants were characterized in vivo in bacteria by flow cytometry and during the entire growth curve by spectrofluorometry. We identify mutations that either increase or decrease the light sensitivity at sub-saturating light intensities, while also improving the light activation and dark-to-light fold change. Notably, light sensitivity and activation levels could be changed independently. In addition, we demonstrated that the shapes of the dose-response curves can be finely tuned. This broadens the applicability of the Magnets photosensors for optogenetic regulation strategies. Photosensory protein domains, derived from nature, are foundational for optogenetic protein engineering. Here the authors develop a high-throughput strategy to tune the light sensitivity and activation of a widely used optogenetic protein system.

Subcellular compartments organize RNAs into phase-separated condensates, significantly influencing RNA metabolism. However, the study of how specific RNAs regulate interacting factors and their phenotypic outcomes is hindered by the lack of advanced imaging and regulation tools. To address this, we developed an orthogonal RNA aptamer system, Clivia-HT, which integrates a fluorescent imager with a ribonuclease-targeting chimera (RIBOTAC) degrader. This platform enables simultaneous RNA visualization and targeted degradation in living cells. Furthermore, we engineered light-activatable and light-inactivatable RIBOTACs to achieve temporal RNA degradation control. Applying this system, we demonstrated that Activating Transcription Factor 4 (ATF4) mRNA localizes to stress granules and regulates their dynamics. We also detected the role of Non-Coding RNA Activated by DNA Damage (NORAD) in RNA–protein condensate assembly. Our approach establishes a versatile method for spatiotemporal RNA manipulation, providing a powerful tool for probing RNA function in dynamic cellular environments. Studying RNA in cellular condensates requires precise tools. Here, the authors developed an orthogonal RNA aptamer system for simultaneous RNA visualization and targeted degradation, revealing new roles for specific RNAs in stress granule and NP body dynamics.