The biotransformation of acetaminophen, a pharmaceutical contaminant widely found in crop produce, in the rice phyllosphere highlights critical xenobiotic-plant-microbiota interactions. This study investigated acetaminophen uptake, translocation, and transformation in hydroponically exposed rice shoots, revealing accumulation at 8.33 ± 0.82 μg/g and conversion into hydroxylated, glycosylated, methylated, thiomethylated, sulfonated, dimerized, and amino acid-conjugated derivatives. Specifically, these transformations may be driven by plant enzymes (cytochrome P450, glycosyltransferases, sulfotransferases, and methyltransferases) and synergistically by enriched microbial genera (Sphingomonas, Pantoea, and Pseudomonas). Furthermore, acetaminophen stress altered the rice phyllosphere metabolome (elevated linoleic acid and jasmonic acid) and reshaped microbial communities, with enhanced degradation pathways and network complexity indicating adaptive stress mitigation. Overall, this integrated transcriptome, metabolome, and microbiome profiling provides mechanistic insights into the cooperative detoxification role of plant enzymes and phyllosphere microbes, offering perspectives on leveraging plant-microbiota interactions to reduce xenobiotic impacts on crops and food safety.

Adaptive, closed-loop control of cellular behavior is essential for next-generation therapies, yet most current treatments operate in an open-loop manner and lack robustness to patient variability and disease dynamics. Here, we establish a control-theoretic platform for rational engineering of closed-loop cell-based therapies that achieve precise and robust regulation. First, we introduce multi-dimensional nullgram profiling, a high-throughput approach that enables quantitative prediction and design of advanced genetic controllers in human cells across circuit topologies and parameter regimes in a single experiment. To evaluate dynamic therapeutic behavior, we next develop Cyberpatient-in-the-loop, an optogenetic digital twin platform that interfaces engineered mammalian cells with computational disease models, enabling systematic testing of closed-loop performance under realistic perturbations. Finally, we leverage these approaches to implement integral feedback cell therapies that sense inflammatory signals and autonomously regulate cytokine levels in primary immune cell cultures. Together, these results establish a general paradigm for engineering cell-based control systems and provide a foundation for next-generation cell therapies.

Internal ribosome entry sites (IRESs) provide compact RNA elements for noncanonical translation and hold promise as building blocks for RNA-based regulation in synthetic biology. However, the cricket paralysis virus (CrPV) IRES shows very low activity in Saccharomyces cerevisiae, limiting its broader utility despite extensive structural and biochemical studies. Here we report a yeast engineering strategy that enhances CrPV IRES-mediated translation by combining host modifications at three mechanistically distinct levels: translation initiation, tRNA modification, and mRNA stability. A reporter-based screen revealed host factors that influence IRES activity and uncovered a trade-off between IRES stimulation and maintenance of cap-dependent translation required for growth. Stepwise integration of nonsense-mediated decay deficiency, a tad3 temperature-sensitive allele, and wild-type eIF4E overexpression yielded a strain with up to an order-of-magnitude increase in reporter output compared with that of the parental strain. These results establish a proof-of-principle framework for host engineering of noncanonical translation.

Some microbes externalize costly biosynthetic precursors in sufficient quantities to sustain a recipient population through cross-feeding. However, it is unclear whether metabolites are externalized purely for a reciprocal benefit or if metabolite externalization also plays a physiological role for the producer. Here we focus on adenine, a metabolite externalized by some strains of the phototrophic bacterium Rhodopseudomonas palustris at sufficient levels to support E. coli growth. In 10 long-term monocultures and 22 cocultures pairing R. palustris with E. coli, extracellular adenine externalized by all 140 isolates screened was 1.7 - 3.4-fold higher than that by the ancestor, suggesting that there was selective pressure for adenine externalization. We hypothesized that adenine is toxic to R. palustris. The CGA0092 growth rate decreased by half in the presence of about 0.3 mM external adenine. This inhibitory effect increased by an order of magnitude when we overexpressed adenine phosphoribosyltransferase to overcome a bottleneck in the purine salvage pathway, suggesting that toxicity stems from a metabolite derived from adenine. To assess whether adenine tolerance is connected to adenine externalization, we surveyed 12 evolved isolates and 49 environmental strains that externalized different levels of adenine, revealing a significant positive correlation. Our data suggests a physiological role for externalization of costly-metabolites like adenine at the origin of cross-feeding. In addition to cross-feeding, resulting metabolic interactions could be negative, considering that even a biosynthetic precursor like adenine can be inhibitory.

DNA has emerged as a promising medium for the post-silicon era of information storage due to its ultrahigh density and longevity. However, current systems are bifurcated, with solid-state systems providing robust cold archival but lacking accessibility, while fluidic molecular computing systems offer dynamic processing but suffer from low density and instability. This mutual exclusivity has hindered the development of hierarchical memory, a standard in modern computing, within molecular storage systems. Here, we bridge this gap by engineering a reconfigurable DNA memory architecture driven by programmable liquid-liquid phase separation (LLPS). Our system leverages sequence-based encoding to achieve an ultrahigh storage density of 7×10^10 GB/g, approaching the theoretical limits of DNA accessibility. In its fluidic hot state, DNA droplets enable rapid data loading (~83.8% in 5 min) and function as an in-memory editing platform supporting versatile, addressable bit-level operations including selective erasure (~65.1%) and high-efficiency rewriting and replacement (>99%) via programmable strand displacement. Importantly, to resolve the stability trade-off, we engineered a programmable phase transition whereby the triggered assembly of a rigid tetrahedral DNA framework (TDF) armor transforms liquid condensates into robust armored droplets. This cold state confers exceptional resistance to enzymatic and physical degradation, projecting multi-millennial data stability. By enabling reversible transitions between an editable, high-density computing mode and a stabilized archival mode, this work establishes the architectural foundation for scalable molecular information storage capable of hierarchical data management.

There is growing interest in engineering animal and plant microbiomes to deliver double-stranded RNA (dsRNA) for RNA interference (RNAi) applications. We developed a genetically encoded biosensor that uses bimolecular fluorescence complementation to monitor dsRNA levels within bacterial cells to accelerate the symbiont-mediated RNAi design-build-test cycle. We validated performance of the sensor in Escherichia coli and demonstrated enhanced dsRNA accumulation in engineered strains of the aphid symbiont Serratia symbiotica.

The release of labile organic carbon (OC) and nutrients during seasonal algal blooms can undermine blue carbon sequestration in coastal ecosystems. Although marine microorganisms mediate OC degradation during macroalgal decay, the underlying mechanisms remain poorly defined. This study employed an integrated multiomics approach (amplicon sequencing, metagenomics, and metatranscriptomics) to investigate microbial regulation of OC degradation and coupled nutrient cycling in coastal sediments with and without decomposing Sargassaceae. Total carbon in sediments increased by over 33% in the Sargassaceae area. Microbial α-diversity in the Sargassaceae area decreased significantly (p < 0.05), while processes linked to OC degradation, carbohydrate metabolism, nitrate (NO3–) reduction, inorganic phosphorus utilization, and sulfur metabolism were significantly upregulated (p < 0.05). Accordingly, gene expression and extracellular hydrolase activities targeting key biopolymers (i.e., cellulose, hemicellulose, starch, and chitin) were significantly upregulated (p < 0.05) in the area with Sargassaceae. Metabolism reconstruction of metagenome-assembled genomes identified Vibrio, Pseudoalteromonas, Alteromonas, and Exiguobacterium_A as primary OC degraders, with genomic capacities enriched in NO3– reduction and assimilatory sulfate reduction. Key environmental drivers─including the C/N ratio, dissolved organic carbon, total dissolved nitrogen (DON), and NO3–─shaped microbial metabolic activities during macroalgal decomposition. Our finding demonstrates that microbially driven OC degradation is a pivotal process coupled with nutrients cycling, advancing the mechanistic understanding of microbial carbon processing and its biogeochemical linkages during macroalgal decomposition in coastal ecosystems.

Orphan genes - genes lacking detectable homologs outside a species - are widespread in microbial genomes and are thought to contribute to their adaptation and molecular innovation. However, not all predicted orphan genes may represent novel functional coding sequences. False positive orphan genes, also called spurious orphan genes, can arise from gene prediction errors. We reason that orphan genes lacking detectable expression are more likely to be spurious. To this end, we combined large-scale metatranscriptomic profiling of the human gut microbiome with machine learning to distinguish expressed orphan genes from spurious ones and to compare them with conserved genes found in multiple species. Using nearly 5,000 metatranscriptome libraries, we identified ~218,000 orphan genes supported by expression evidence, while ~330,000 predicted orphan genes lacked detectable expression, and were classified as spurious. We extracted 154 sequence, structural, and evolutionary features for each gene and trained XGBoost classifiers while accounting for genomic representation. The models achieved an area under the receiver operating characteristic curve (AUC) of 0.82 in distinguishing expressed orphan genes from spurious orphan genes and 0.93 in distinguishing expressed orphan genes from conserved genes. SHAP-based interpretation revealed clear biological signals. E.g., expressed orphans were present in more genomes than spurious ones and expressed orphan genes were shorter than conserved genes. This work improves orphan gene discovery and suggests that expressed orphan genes differ systematically from conserved genes and spurious orphan genes in sequence composition, structural constraints, and evolutionary signals.

Life on Earth has long been regarded as homochiral, relying almost exclusively on a single enantiomer of sugars, typically the D-form. However, recent discoveries challenge this paradigm, including the identification of L-glucose-catabolizing bacteria and microbial L-glucoside hydrolases. Despite these findings, the metabolic diversity of organisms toward a broader range of atypical sugar enantiomers and their ecological relevance remains largely unexplored. This study aimed to identify and isolate microorganisms capable of catabolizing atypical enantiomers of diverse sugars. We performed enrichment cultures with either the D- or L-forms of glucose, fructose, xylose, and sorbose, using soil and activated sludge as microbial sources. Microbial growth was observed under all tested conditions, with the dominant taxa varying depending on the sugars supplied. Six phylogenetically distinct bacterial isolates exhibited the ability to catabolize atypical sugar enantiomers, two of which exhibited growth on all tested sugars. These findings uncover a previously unrecognized diversity in microbial sugar metabolisms, providing new insights into the environmental dynamics of atypical sugar enantiomers and offering a novel perspective on the principle of biological homochirality. Furthermore, this work lays a foundation for the development of biomanufacturing processes using racemic sugar mixtures synthesized via abiotic chemical reactions.