DNA sliding clamps are central coordinators of genome replication and maintenance, yet the full binding network (“interactome”) of the bacterial β-clamp remains incompletely defined. Here, we report a novel interaction between E. coli β-clamp and the helicase-nuclease RecBCD complex. Using bacterial two-hybrid assays and co-immunoprecipitation, supported by fluorescence microscopy, we show that RecB associates with β-clamp. Nuclear magnetic resonance spectroscopy maps the interaction to the canonical ligand pocket of β-clamp and identifies a clamp-binding motif in RecB (residues 1018–1023, QVEMEF), whose mutation abolishes binding. Functional assays indicate that this interaction occurs upon conformational switching of RecBCD at a Chi site, and disruption of the motif reduces survival after DNA damage. We also find indications of a second binding site in the helicase domain of RecB. These findings expand the β-clamp interactome and suggest a previously unappreciated role for β-clamp in DNA double-strand break repair, with potential implications for antibacterial strategies.

Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolize it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring–summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.

Soil sulfur cycling plays a central role in ecosystem functioning and is tightly coupled to carbon–nitrogen–phosphorus–metal cycling. Key transformations occur at interfaces where microbes, minerals, and organic matter interact, yet these processes remain insufficiently resolved across scales and systems. Here, we synthesize evidence from multi-omics, isotopic tracing, and nanoscale spectroscopy and imaging to develop a microbial–mineral–organic matter interaction framework linking redox microdynamics, mineral reactivity, organic matter chemistry, and microbial guilds to sulfur speciation and turnover. We show how anthropogenic disturbance and climate change reshape interface-centered sulfur biogeochemical networks, with implications for nutrient retention, pollutant transport, and greenhouse gas emissions. We further identify major research hotspots, examine boundary conditions, and outline an artificial intelligence–process hybrid strategy for mechanism-based prediction and sustainable soil management under accelerating global change. This framework helps connect interface-scale mechanisms with ecosystem-scale consequences and provides a basis for future cross-system testing. Across soil systems, sulfur cycling is shaped by the interplay among microbial functional guilds, mineral reactivity, organic sulfur chemistry, and fluctuating physicochemical conditions, based on a framework of microbial–mineral–organic matter interactions.

Functional genomics have been hampered by the paucity of efficient methods that connect genotype and metabolic phenotype at single-cell resolution. Using the industrial microalga Nannochloropsis oceanica as a model, we introduced a platform that comprises a genome-wide single-gene-edited mutant library and high-throughput Raman-activated cell sorting (RACS). The CRISPR/Cas-generated library consisted of 3567 microalgal mutants derived from 2397 effective guide RNAs. Label-free sorting of the library for high carotenoid content by RACS unraveled mutations in the violaxanthin de-epoxidase (noVDE) or in the proteasome assembly chaperone 4 (noPAC4) genes. Knocking out all five known noVDEs revealed that the high carotenoid content is due to violaxanthin increase, whilst noPAC4 knockout boosted carotenoid content with elevations in violaxanthin, zeaxanthin, and β-carotene. Genetic and transcriptomic evidence suggested two previously unknown modes of carotenogenesis regulation mediated by noPAC4: epigenetic mechanisms via histone deacetylase (HDAC) and post-translational controls by the 26S proteasome. Therefore, by label-freely sorting single-cell metabolic phenotype and rapidly yet unambiguously tracing it to a genotype, this forward-genetics approach can greatly accelerate the discovery of genes and pathways. Functional genomics in algae are limited by efficient methods that connect genotype and metabolic phenotype at single-cell resolution. Here the authors introduce an approach based on a genome-wide mutant library and a Raman Cytometer, discovering a carotenoid synthesis regulating pathway.

The precise translational control of gene expression by small molecules through RNA-based switches holds considerable promise for both research and therapeutic developments. However, current high-performance RNA switches remain limited in adaptability, with strong responses typically constrained to a narrow set of specific ligand-aptamer pairs. To address this limitation, we introduce a robust and generalizable RNA platform based on a multivalent aptamer design, which significantly enhances ligand-responsive protein expression through alternative splicing regulation. We have demonstrated that the inherently weak aptamers, such as those for theophylline or tetracycline, can be dramatically improved through this multivalency circuit, elevating the induction levels from modest (<10-fold) to over 100-fold, an increase of more than an order of magnitude. Leveraging these improved switches, we achieve multiplex and orthogonal control over distinct protein outputs with these suboptimal aptamers. Furthermore, we implement precise manipulation of cellular phenotypes through the ligand-controlled expression of functional proteins, including the pro-apoptotic effector BAX and the adhesion protein E-cadherin. This work establishes a general and adaptable RNA platform for expanding the toolbox of small-molecule regulators of protein expression, with potential applications across synthetic biology and therapeutic applications.

RNA devices, including riboswitches, aptazymes, and RNA-based biosensors, have become essential components in synthetic and molecular biology. These systems make use of RNA’s modularity and structural diversity to build programmable tools for sensing, regulation, and cellular computation. To drive these systems, RNA aptamers usually need to undergo a conformational change upon ligand binding. However, the limited availability of such aptamers has restricted the development and application of RNA devices, particularly in mammalian systems. Traditional selection methods often prioritize high-affinity binding, resulting in a scarcity of conformation-switching aptamers. Here, we addressed this limitation by selecting a caffeine-binding aptamer with RNA Capture-SELEX and in vivo screenings. This aptamer functioned as a modular regulator of riboswitches and ribozymes in Saccharomyces cerevisiae and mammalian cells. Through new optofluidic screenings, we overcame throughput and sequence-function challenges inherent in ribozyme screening for mammalia. Additionally, a straightforward grafting method transformed the aptamer into a fluorogenic iSpinach aptasensor. This work demonstrates the successful selection of a modular and communicating aptamer for a challenging target like caffeine and establishes robust strategies for their modular integration into diverse RNA platforms. These strategies pave the way for broadening the repertoire of aptamers and expanding the potential of RNA-based synthetic biology.

Microbial communities are often more species-rich than predicted from classical ecological models. The high levels of coexistence observed in nature are typically attributed to forces that modulate niche availability and stabilize communities. Specific drivers of niche partitioning are often tested in isolation, and the interactive effects of niche variation across resources, space, and time have not been tested together experimentally to determine how they affect community responses. Here, we used 26 bacterial strains previously isolated from carnivorous pitcher plant (Sarracenia purpurea) aquatic pools to construct and expose species-rich synthetic communities to four factors that alter environmental complexity in a fully factorial design, creating combinations of resource complexity, spatial niche structure, and temporal fluctuations. Across treatments, increased niche complexity generally, but not always, promoted the long-term retention of more species, with a saturating effect at the highest levels of complexity. Resource complexity emerged as a primary driver of diversity, with its effects also depending on other niche axes. Interactions among factors frequently deviated from additive expectations, with both synergistic and antagonistic effects observed depending on the combination of conditions. Together, these results show that environmental complexity shapes bacterial diversity through context-dependent, nonlinear interactions among niche dimensions, highlighting that the relationship between niche dimensionality and diversity is contingent on how environmental factors combine.

Microbial cell factory is a powerful biological tool for synthesizing value-added molecules due to its unmatched sustainability and selectivity. However, the inherent catalytic specificity of natural enzymes limits product diversity. Although photobiocatalysis has expanded enzyme catalytic capabilities, challenges such as laborious enzyme purification, incompatibility with in vivo conditions, and complex unnatural substrate synthesis hinder photobiomanufacturing efforts. Herein, we combine a microbial cell factory with a new-to-nature photobiocatalytic transformation via a modular design that combines aerobic fermentation (Module I) and anaerobic photocatalysis (Module II) to achieve de novo biosynthesis of d-homotryptophan. In Module I, we engineer E. coli equipped with a biosynthetic gene cluster to produce indole-3-acetic acid (IAA) via modifying metabolic flux and multi-copy genetic amplification strategies. In Module II, we develop an efficient synergistic photoredox/enzymatic synthesis of d-homotryptophan from l-serine and IAA by a pyridoxal phosphate (PLP)-dependent tryptophan synthase beta-subunit (TrpB) variant. This work synergistically merges emerging photobiocatalytic reactivity with natural biosynthesis, demonstrating a platform with potential for future biomanufacturing of non-natural products. Microbial cell factories are a powerful tool for synthesizing value-added molecules, but the inherent catalytic specificity of natural enzymes limits product diversity. Here, the authors combine a microbial cell factory with a new-to-nature photobiocatalytic transformation via a modular design that combines aerobic fermentation and anaerobic photocatalysis to achieve de novo biosynthesis of d-homotryptophan.