The plant microbiome plays a crucial role in enhancing disease resistance, yet microbiome-based plant protection strategies remain limited by an incomplete understanding of how host selection, microbial interactions, and rhizosphere chemistry jointly shape pathogen suppression. Here, we adopt a “learning from nature” approach to design synthetic microbial communities (SynComs) that recapitulate naturally evolved disease-suppressive interactions, using banana Fusarium wilt as a model system. High-throughput profiling revealed that both bacterial and fungal communities contribute to varietal resistance. Resistance-associated microbial taxa were identified and isolated to assemble bacterial, fungal, and cross-kingdom SynComs representative of resistant versus susceptible hosts. SynComs derived from resistant varieties suppressed pathogen growth more effectively than those from susceptible hosts, with cross-kingdom SynComs exhibiting the strongest effects. Cross-kingdom SynCom inoculation significantly reduced disease severity and restructured both the composition and functional potential of the rhizosphere microbiome. Integrative transcriptomic and metabolomic analyses revealed coordinated host metabolic reprogramming, characterized by increased accumulation of diverse metabolites, including alkaloids, amino acids, and flavonoids. Notably, supplementation with resistance-associated rhizosphere metabolites, such as stearic acid and shikimic acid, further enhanced disease suppression. Together, our findings establish a mechanistic framework in which host-guided microbiome assembly and metabolite-mediated interactions jointly enable effective cross-kingdom SynComs for disease suppression, providing ecological principles for microbiome-based plant protection strategies.

Since its discovery, the CRISPR-Cas system has ushered in a transformative era in biodetection, leveraging its simplicity and efficiency to enable Cas protein-based signaling systems for applications in early tumor screening, viral detection, and molecular logic circuits. However, the constrained compatibility of CRISPR/Cas-based signaling systems with diverse input types limits their versatility, primarily due to the restricted activation mechanisms of the Cas protein. Herein, we developed the Cas12a and Cas13a Integrated Targeting (CACIT) system, which harnesses DNA/RNA strand displacement reactions to integrate the enzymatic capabilities of Cas12a and Cas13a. This system supports simultaneous DNA and RNA inputs, offering exceptional programmability and cost-effectiveness. By employing strand displacement reactions, the CACIT system achieves synchronized activation of Cas12a and Cas13a. We have demonstrated that the CACIT system excels in single-nucleotide-variant (SNV) detection, viral RNA detection, machine learning-driven nucleic acid concentration response modeling, logic operations, and intracellular imaging. As a streamlined and versatile signaling platform, the CACIT system expands the scope of CRISPR/Cas activation strategies. With its inherent simplicity and compatibility, this system facilitates integration with diverse nanodevices. Further, this system provides a highly programmable, multifunctional computational module for molecular networks, heralding new possibilities for artificial signaling systems.

Adenosine triphosphate (ATP) hydrolysis is the main cellular source of energy used to drive biochemical reactions that are otherwise energetically unfavorable. The chemical energy stored in phosphoanhydride bonds is released upon hydrolysis of ATP to ADP and is used to drive mechanical work and conformational change. DNA replication is a canonical process in which the multi-enzyme replisome is thought to rely on ATP hydrolysis for its function. Here we show, through single-molecule visualization of DNA replication by the E. coli replisome, that the replicative DnaB helicase does not rely on hydrolysis of ATP in the context of the elongating replisome. Even in the presence of physiologically-relevant concentrations of ATP, dTTP is hydrolysed preferably. Finally, we show that the replicative helicases from S. cerevisiae, D. melanogaster, and Homo sapiens can also use dTTP to unwind DNA. Our observations suggest that replicative helicases across domains of life are ‘flex-fuel’ helicases. Here the authors show that replicative helicases from bacteria to humans can use dTTP instead of ATP for DNA unwinding, and that the E. coli replisome preferentially uses dTTP during DNA replication, challenging textbook models of replication energetics.

Protease-mediated activation of immune effectors is an evolutionarily conserved mechanism. This study identifies a widespread trypsin–MBL (metallo-β-lactamase) module as a core effector in diverse antiviral bacterial immune systems, such as Hachiman, AVAST and Argonaute. Focusing on the Hachiman-associated trypsin–MBL system, we show that trypsin•HamAB protease activity is inhibited by ATP, while MBL is an autoinhibited DNase with two insertion loops obstructing its catalytic site. Upon infection, trypsin•HamAB senses foreign DNA and hydrolyzes ATP, activating trypsin-like activity, which specifically cleaves MBL at the insertion loops to release repression. The activated MBL depletes DNA and arrests host cell growth. Cryo-electron microscopy structures of trypsin•HamAB–DNA reveal that DNA binding and ATP hydrolysis trigger HamAB oligomerization and trypsin-like domain release, enabling its activation. Our work elucidates a conserved immune mechanism wherein proteolytic activation of a nuclease enables robust immunity against phage while multilayered controls prevent self-toxicity, expanding the repertoire of immune processes governed by regulatory proteolysis. This study identifies and characterizes a conserved trypsin–MBL (metallo-β-lactamase) pair in bacterial immunity; upon infection, trypsin is activated through inhibitory ATP hydrolysis, subsequently activating MBL through site-specific proteolysis, which depletes DNA and restricts cell growth.

Gene expression is controlled by transcription factors (TFs), whose genome binding is shaped by chromatin accessibility and histone modifications, yet mapping these interactions, particularly those with weak affinity or a transient nature, in single cells remains technically challenging. To address this gap, we developed docking and deamination followed by sequencing (D&D-seq), a single-cell immuno-tethering technology for profiling DNA-protein interactions. D&D-seq couples an antibody-binding nanobody to a cytosine base editor, a combination that enables detection of weak or transient factor binding through targeted cytosine-to-uracil editing at protein-bound genomic sites. This approach is compatible with standard single-cell multi-omic workflows and therefore allows integrated analyses of gene regulation. Using assay for transposase-accessible chromatin using sequencing (ATAC-seq) and single-cell ATAC-seq (scATAC-seq), we assessed chromatin accessibility as a functional readout of TF activity, and by coupling D&D-seq with whole-genome sequencing, we captured CTCF binding in both active and inactive chromatin compartments.

Arsenic (As), a toxic element widespread in paddy soils worldwide, is mobilized by microbial processes, posing risks to environmental quality, food safety and human health. The rice rhizosphere is a dynamic environment with day–night cycles in chemical conditions and microbial activity. However, how arsenic itself changes over these daily cycles remains unexplored. Here we conduct metatranscriptomic and biogeochemical analyses in a greenhouse study to investigate the diurnal rhythms of As dynamics in the rice rhizosphere. We observed consistent diel fluctuations in arsenite (As(III)) concentrations, increasing from 1.8 to 2.9 mg l‒1 at night, alongside a 24.9% rise in ferrous iron (Fe(II)). Redox potential decreased to ~100 mV at night, promoting As/Fe reduction. Transcriptional activity of key functional genera involved in dissimilatory As/Fe reduction (for example, Geomobilimonas and Geobacter) increased at night, reflected in higher transcript abundances of reduction genes (arrA, omcS, omcZ and mtrC), without corresponding changes in relative abundance. These patterns were confirmed in a field study. Under constant darkness, these diel patterns disappeared. Together, these findings suggest managing rice cultivation to align with natural daily cycles may reduce contamination risks and optimize nutrient management. Diurnal cycles in microbial reducer activity reveal synchronized mobilization of arsenic and iron in the rice rhizosphere, as shown by metatranscriptomic and biogeochemical analyses.