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August 28, 12:41 PM
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New microbial hosts with superior phenotypes, such as fast growth, are attractive for research and biotechnology, but often lack systematic evaluation of functional genetic parts. A reference set of working plasmids would increase reproducibility and encourage use of these hosts. Here, we use the POSSUM toolkit, a collection of 23 origins-of-replication and 6 antibiotic markers, to identify functional genetic parts for strains of Vibrio natriegens. We applied this to the wild-type strain ATCC 14048 and an engineered variant NBx CyCloneTM, evaluating 414 combinations of origins of replication and antibiotic selection conditions. We show that both strains support five replicons (pNG2, pSa, pSC101ts, p15A, and RSF1010) with NBx CyCloneTM supporting an extra replicon RK2. The assay can be performed in under a week and is compatible with multiple DNA delivery methods. This work demonstrates the feasibility of rapidly establishing reference information to accelerate the adoption of new microbial hosts.
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August 28, 12:16 PM
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Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know little about how de novo promoters emerge in genomic DNA, especially compared to random DNA that has never been subjected to selection. Here, we assayed the promoter activity of 17,129 random, synthetic DNA sequences and 91,866 E. coli genomic DNA sequences. Genomic DNA encodes ~1.3 times more promoters than random DNA. We then studied 584,573 point mutations in 225 random and 60 genomic sequences, and asked how they cause the emergence of de-novo promoters. We find that de-novo promoters emerge ~3 times more readily from random DNA than from genomic DNA. The reason is that the genome contains fewer proto-binding sites for transcriptional activators than random DNA. Our work shows that the evolutionary history of a DNA sequence introduces substantial biases in its evolutionary potential, especially in the likelihood that mutations create new and potentially adaptive transcripts.
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August 28, 12:02 PM
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Oscillations are fundamental to biological timekeeping and organization, yet understanding how their complex temporal dynamics emerge from underlying molecular interactions remains a significant challenge. In vitro reconstitution offers a powerful bottom-up approach to dissect the minimal components, interactions, and parameters required to generate these rhythmic behaviors. Biochemical reconstruction of minimal oscillators outside of their native cellular contexts allows the direct interrogation of the biochemical, biophysical, and systems-level properties that govern oscillatory dynamics and unravel the governing fundamental design principles. In this review, we summarize the theoretical foundations of biological oscillators and outline the major experimental challenges associated with their in vitro reconstitution. We highlight recent advances in the reconstitution of diverse oscillator types, including the cyanobacterial circadian clock, the Min system from Escherichia coli, and synthetic genetic oscillators such as the repressilator. These case studies illustrate how reconstitution efforts have yielded key mechanistic insights and driven technological innovation. We conclude by exploring emerging tools and future directions that promise to overcome current limitations and broaden the applicability of oscillator reconstitution–both to additional biological systems and to a wider range of scientific questions.
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August 28, 11:56 AM
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The determination of RNA secondary structure (RSS) could help understand RNA’s functional mechanisms, guiding the design of RNA-based therapeutics, and advancing synthetic biology applications. However, traditional methods such as NMR for determining RSS are typically time-consuming and labor-intensive. As a result, the accurate prediction of RSS remains a fundamental yet unmet need in RNA research. Various deep learning (DL)-based methods achieved improved accuracy over thermodynamic-based methods. However, the over-parameterization nature of DL makes these methods prone to overfitting and thus limits their generalizability. Meanwhile, the inconsistency of RSS predictions between these methods further aggravated the crisis of generalizability. Here, we propose TrioFold to achieve enhanced generalizability of RSS prediction by integrating base-pairing clues learned from both thermodynamic- and DL-based methods by ensemble learning and convolutional block attention mechanism. TrioFold achieves higher accuracy in intra-family predictions and enhanced generalizability in inter-family and cross-RNA-types predictions. Additionally, we have developed an online webserver equipped with widely used RSS prediction algorithms and analysis tools, providing an accessible platform for the RNA research community. This study demonstrated new opportunities to improve generalizability for RSS predictions by efficient ensemble learning of base-pairing clues learned from both thermodynamic- and DL-based algorithms.
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August 28, 11:50 AM
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Aromatic compounds are vital in both natural and synthetic chemistry, and they are traditionally sourced from non-renewable petrochemicals. However, plant biomass, particularly lignin, offers a renewable alternative source of aromatic compounds. Lignin, a complex polymer found in plant cell walls, is the largest renewable source of aromatic compounds, though its degradation remains challenging. Lignin can be chemically degraded through oxidation, acid hydrolysis or solvolysis. As an alternative, microorganisms, including fungi, could offer a sustainable alternative for breaking down lignin. The aromatic compounds released from lignin, by either microbial, chemical or enzymatic degradation, can be used by microorganisms to produce valuable compounds. Fungi possess unique enzymes capable of converting aromatic compounds derived from lignin or other sources into chemical building blocks that can be used in several industries. However, their aromatic metabolic pathways are poorly studied compared to bacterial systems. In the past, only a handful of genes and enzymes involved in the aromatic metabolic pathways had been identified. Recent advances in genomics, proteomics, and metabolic engineering are helping to reveal these metabolic pathways and identify the involved genes. This review highlights recent progress in understanding fungal aromatic metabolism, focusing on how Aspergillus niger converts plant-derived aromatic compounds into potentially useful products and the versatility of aromatic metabolism within the Aspergillus genus. Addressing the current knowledge gaps in terms of fungal pathways could unlock their potential for use in sustainable technologies, promoting eco-friendly production of chemical building blocks from renewable resources or bioremediation.
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August 28, 11:44 AM
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The recent discovery of TIGR-Tas (Tandem Interspaced Guide RNA-Targeting Systems) marks a major advance in the field of genome editing, introducing a new class of compact, programmable DNA-targeting systems that function independently of traditional CRISPR-Cas pathways. TIGR-Tas effectors use a novel dual-spacer guide RNA (tigRNA) to recognize both strands of target DNA without requiring a protospacer adjacent motif (PAM). These Tas proteins introduce double-stranded DNA cuts with characteristic 8-nucleotide 3′ overhangs and are significantly smaller than Cas9, offering delivery advantages for in vivo editing. Structural analyses reveal homology to box C/D snoRNP proteins, suggesting a previously unrecognized evolutionary lineage of RNA-guided nucleases. This review positions TIGR-Tas at the forefront of a new wave of RNA-programmable genome-editing technologies. In parallel, I provide comparative insight into the diverse and increasingly modular CRISPR-Cas systems, including Cas9, Cas12, Cas13, and emerging effectors like Cas3, Cas10, CasΦ, and Cas14. While the CRISPR-Cas universe has revolutionized molecular biology, TIGR-Tas systems open a complementary and potentially more versatile path for programmable genome manipulation. I discuss mechanistic distinctions, evolutionary implications, and potential applications in human cells, synthetic biology, and therapeutic genome engineering.
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August 27, 10:32 PM
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Microbial-assisted restoration (MaR) is gaining traction, yet its outcomes under recurring and extreme drought remain uncertain. We propose that ecological debt – functional erosion from trade-offs between stress tolerance and performance – can limit MaR success. By linking this debt to microbial coalescence dynamics, we offer a framework to improve microbiome-based restoration under climatic stress.
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August 27, 10:13 PM
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Root exudation is an important trait that enables plants to shape their interactions with soil-borne organisms. Amino acids present in root exudates play important roles in bacterial chemotaxis, bacterial metabolism, and root colonization, contributing to plant nutrition and health. Notwithstanding the importance of amino acids in shaping the rhizosphere microbiome, the identities of the plant amino acid transporters that mediate their root exudation have remained elusive. Here, we report that the Arabidopsis UMAMIT30 transporter, robustly expressed in root and shoot tissues, significantly contributes to amino acid root exudation. umamit30 loss-of-function mutants were compromised for amino acid root exudation as shown by the low concentration of amino acids, particularly glutamine, recovered from root exudates compared to wild-type plants. Amino acid quantification, as well as uptake and secretion assessments using radiolabelled glutamine, revealed that the shoots of umamit30 accumulate amino acids and have a reduced capacity to secrete glutamine, impacting root exudation. Our results identify UMAMIT30 as a broadly specific amino acid exporter strongly expressed in Arabidopsis vasculature. Loss-of-function mutants displayed reduced amino acid levels in root exudates, with significant drops in glutamine and asparagine among others, yet exhibited no detectable growth defects. UMAMIT30 disruption led to elevated shoot amino acid content and reduced glutamine efflux from shoots, suggesting a role in phloem uploading rather than root exudation alone. Despite decreased levels of root exuded amino acids, beneficial Pseudomonas interactions and plant-growth-promotion remained unaffected.
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August 27, 2:27 PM
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Rhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging. Here, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla. Genomic analysis of the individual strains was performed to reveal encoded plant growth-promoting traits, including genes for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ transporters, and some predicted traits were validated by laboratory phenotypic assays. The SynCom demonstrates strong stability both in vitro and in planta. Most strains encoded multiple plant growth-promoting functions, and several of these were confirmed experimentally. The presence of osmoprotectant and ion transporter genes likely contributed to the observed resilience of Brachypodium to drought stress, where plants amended with the SynCom recovered better than those without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria. Our results demonstrate that trait-informed construction of synthetic communities can yield stable, functionally diverse consortia that enhance plant resilience under drought. Preferential colonization near root tips points to active, localized plant–microbe signaling as a component of stress-responsive recruitment. This stable SynCom provides a scalable platform for probing mechanisms of plant-microbe interaction and for developing microbiome-based strategies to improve soil and crop performance in variable environments.
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August 27, 12:40 PM
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Researchers have created glow-in-the-dark plants by injecting succulents with materials similar to those that make the posters light up. The fleshy plants shine as brightly as a night light, and can be made to do so in a wide variety of colours — a first for glowing houseplants, according to the team. The researchers, led by Xuejie Zhang, a materials scientist describe today how they produced the plants in the journal Matter1. The idea of making glowing plants has captivated scientists since the late 1980s, when researchers made the first bioluminescent plant2 by inserting a gene from a firefly (Photinus pyralis) into a type of tobacco (Nicotiana tabacum). This work laid the foundation for the first genetically engineered luminescent houseplant to come on the market in the United States, last year. The biotechnology firm Light Bio in Sun Valley, Idaho, sells the petunia (Petunia hybrida), which glows a very faint green thanks to genes from a light-emitting mushroom. the succulent glows because of materials injected into its leaves. These materials — phosphor particles made of strontium and aluminium dosed with other metals — absorb energy from light at one wavelength, store some of that energy and then slowly re-emit it at a different wavelength for several hours.
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August 27, 12:17 PM
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Modular polyketide synthases (PKSs) can produce various secondary metabolites in a collinearity fashion. Although rational engineering of modular PKS can ultimately create a diverse array of compounds, de novo generation of defined structures usually results in the loss or remarkable decline of productivity due primarily to the incompatibility of different elements. Here, we present a modular PKS engineering strategy driven by an evolutionary event of gene conversion to accomplish successive engineering of the modular PKS in cinnamomycin biosynthetic gene cluster (cmm BGC). By simulating the gene conversion process, cmm BGC is consecutively reprogrammed to generate a macrolide with predicted structural features. Moreover, the intra-module KS domain is demonstrated to associate with the proofreading of extender units. Collectively, the gene conversion-associated approach may shed a light on modular PKS engineering. Engineering of modular polyketide synthases (PKS) can create natural product derivatives, however, de novo generation of defined structures with good productivity remains challenging. Here, the authors employ a gene conversion-driven strategy to reprogram the cinnamomycin biosynthetic gene cluster, successfully generating a series of new macrolides with designed structural features and highlighting the role of the KS domain in extender unit proofreading.
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August 27, 10:39 AM
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Virus-encoded auxiliary metabolic genes (AMGs) are non-essential genes that increase viral fitness by maintaining or manipulating host metabolism during infection. AMGs are intriguing from an evolutionary perspective, as most viral genomes are highly compact and have limited coding capacity for accessory genes. Advances in viral (meta)genomics have expanded the detection of putative AMGs from viruses in diverse environments. However, this has also led to many instances of misannotation due to the limitations of annotation tools, resulting in misinterpretations about the roles of some viral genes. Here, we highlight studies that support claims about AMGs with more than just function predictions for guidance on best practices. We then propose the adoption of an expanded, inclusive view of all genes auxiliary to core viral functions with the term ‘auxiliary viral genes’ (AVGs), alongside an associated eco-evolutionary framework for considering the types of analyses that can better support claims made about AVGs. This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.
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August 27, 9:55 AM
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Circadian clocks are biological timekeeping mechanisms that synchronize physiology with the 24-h day–night cycle and provide temporal order to cellular events that recur daily as circadian rhythms. The cyanobacterium Synechococcus elongatus displays robust circadian rhythms and for more than 30 years has served as a model organism for uncovering the principles of prokaryotic timekeeping. The fundamental driving force behind these rhythms is a three-protein oscillator composed of KaiA, KaiB, and KaiC. In this review, we summarize current knowledge of the molecular mechanism of the Kai oscillator and focus on the dynamic conformational changes of these proteins over the period of a day. We also discuss how timing information is relayed from the oscillator to regulate downstream gene expression, thereby influencing cellular physiology. Furthermore, we explore circadian or circadian-like timing systems identified in other prokaryotes. We hope this review can inspire the discovery of new clock mechanisms in the microbial world and beyond.
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August 28, 12:38 PM
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Programmable DNA integration using CRISPR-associated transposons (CASTs) offers powerful capabilities for genome engineering. The single effector Cas12k CAST examples evolved from a fixed guide TnpB nuclease protein. Here, we engineer de novo RNA-guided transposition systems, where the single guide RNA effector components are repurposed nuclease-dead TnpB-family proteins. These compact systems mediate high-efficiency guide RNA-directed DNA insertion with preserved orientation control and target immunity, reduced off-site targeting, release of a host factor requirement, and can be paired with an exonuclease domain to mediate cut-and-paste transposition. In this engineered context, the TnpB derivatives show features not predicted from the original enzymes suggesting untapped avenues for improvement. In parallel, we show that mutations at the TniQ-TnsC interface in the Cas12k CAST system selectively attenuate off-site insertions while enhancing on-site activity. These results establish how Cas12 proteins and antecedent TnpB proteins can be engineered for high performance and specificity with guide RNA directed systems.
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August 28, 12:07 PM
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New reference genomes and transcriptomes are increasingly available across the tree of life, opening new avenues to tackle exciting questions. However, there are still challenges associated with annotating genomes and inferring evolutionary processes and with a lack of methodological standardization. Here, we propose a new workflow designed for evolutionary analyses to overcome these challenges, facilitating the detection of recombination suppression and its consequences in terms of rearrangements and transposable element accumulation. To do so, we assemble multiple bioinformatic steps in a single easy-to-use workflow. We combine state-of-the-art tools to detect transposable elements, annotate genomes, infer gene orthology relationships, compute divergence between sequences, infer evolutionary strata (i.e. footprints of stepwise extension of recombination suppression) and their structural rearrangements, and visualise the results. This workflow, called EASYstrata, was applied to reannotate 42 published genomes from Microbotryum fungi. We show in further case examples from a plant and an animal that we recover the same strata as previously described. While this tool was developed with the goal to infer divergence between sex or mating-type chromosomes, it can be applied to any pair of haplotypes whose pattern of divergence is of interest. This workflow will facilitate the study of non-model species for which newly sequenced phased diploid genomes are becoming available.
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August 28, 11:59 AM
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Plants must contend with oxidative stress, a paradoxical phenomenon in which reactive oxygen species (ROS) can cause cellular damage while also serving as key signaling molecules. Environmental stressors, such as drought, salinity, and temperature extremes, promote ROS accumulation, affecting plant growth and productivity. To maintain redox homeostasis, plants rely on antioxidant systems comprising enzymatic defenses, such as superoxide dismutase, catalase, and ascorbate peroxidase, and non-enzymatic molecules, including ascorbate, glutathione, flavonoids, and emerging compounds such as proline and nano-silicon. This review provides an integrated overview of antioxidant responses and their modulation through recent biotechnological advances, emphasizing the role of emerging technologies in advancing our understanding of redox regulation and translating molecular insights into stress-resilient phenotypes. Omics approaches have enabled the identification of redox-related genes, while genome editing tools, particularly those based on clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, offer opportunities for precise functional manipulation. Artificial intelligence and systems biology are accelerating the discovery of regulatory modules and enabling predictive modeling of antioxidant networks. We also highlight the contribution of synthetic biology to the development of stress-responsive gene circuits and address current regulatory and ethical considerations. Overall, this review aims to provide a comprehensive perspective on molecular, biochemical, and technological strategies to enhance oxidative stress tolerance in plants, thereby contributing to sustainable agriculture and food security in a changing climate.
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August 28, 11:53 AM
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Precise control of protein translocation is essential for synthetic biology and protein engineering. Here, we present a temperature-responsive system using elastin-like polypeptides (ELPs) to regulate the translocation of a conditionally lethal enzyme in Escherichia coli. The enzyme, levansucrase, whose activity becomes lethal in the presence of sucrose, was engineered with an N-terminal signal peptide and a C-terminal ELP tag. At 37 °C, the ELP tag induced intracellular aggregation of the fusion protein, preventing its secretion and allowing cell survival, as indicated by translucent colony formation. In contrast, at 16 °C, the ELP remained soluble, permitting levansucrase secretion into the medium. The resulting conversion of sucrose into levan by the secreted enzyme led to host cell death. These findings highlight ELP-mediated aggregation as a reversible and tunable strategy for regulating protein localization and secretion in E. coli, with potential applications in synthetic biology, metabolic engineering, and biocontainment systems.
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August 28, 11:47 AM
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There is currently a pressing issue of antimicrobial resistance, with numerous pathogenic superbugs continually emerging, posing significant threats to both human health and the economy. However, the development of new antibiotics has not kept up in pace with the development of microbial resistance, necessitating the exploration of more effective approaches to combat microbes. Synthetic biology offers a novel paradigm by employing selective screening and assembling diverse biological components to redesign biological systems that can specifically target and eliminate microbes. In particular, engineering living therapeutics enables the detection and precise eradication of pathogenic microorganisms in a controlled means. This review provides an overview of recent advancements in engineering living therapeutics using synthetic biology for antibacterial treatment. It focuses on modifying bacteriophages, microbes, and mammalian cells through engineering approaches for antibacterial therapy. The advantages of each approach are delineated along with potential challenges they may encounter. Finally, a prospective outlook is presented highlighting the potential impact and future prospects of this innovative antimicrobial strategy.
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August 27, 10:49 PM
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The accuracy of enzyme kinetic parameters, particularly the turnover number (kcat), is critical for the predictive power of enzyme-constrained genome-scale metabolic models (ecGEMs). However, current kinetic datasets remain sparse and often fail to capture in vivo enzyme behavior, compromising model predictive capacity. To address these challenges, we developed EnzymeTuning, a generative adversarial network (GAN)-based framework for the global kcat optimization. This approach significantly enhances both the accuracy and proteome-level coverage of ecGEM predictions. Moreover, by incorporating literature-derived protein degradation constants (kdeg), we inferred the protein synthesis rate and systematically evaluated their impact on model performance. The framework was validated across distinct yeast species, including Saccharomyces cerevisiae, Kluyveromyces lactis, Kluyveromyces marxianus, and Yarrowia lipolytica, demonstrating its generalizability. Further, we found that EnzymeTuning facilitates the identification of context-specific enzyme usage patterns and adaptive catalytic resource allocation under varying carbon-to-nitrogen (C/N) ratios, showcasing the substantial potential of our toolbox for integrative omics analysis. Overall, EnzymeTuning provides a robust and scalable solution for refining kinetic parameters in ecGEMs, thereby promoting the wide applications of these computational models in systems and synthetic biological studies.
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August 27, 10:27 PM
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Current gene circuits designed to time gene expression depend on the intricate interactions among various regulators and their targets, which confines them to a limited range of temporal tunability. Here, we report a programmable timer switch of gene expression termed BioFuse, which allows the reaction time ranging from hours to days. BioFuse comprises a series of fuse-like tandem DNA cassettes that can be sequentially edited by the adenine base editors (ABEs), resulting in either the activation or deactivation of a downstream gene once the editing is complete. Adjusting the number of DNA cassettes incorporated allows precise programming of BioFuse’s reaction time. Applying BioFuse to control carotenoid biosynthesis genes decouples lycopene production from growth in E. coli and increases lycopene yield without external inducers. Using BioFuse in a bacterial autolysis system enables timely and efficient protein release. BioFuse offers a versatile tool for precise, wide-range timing of gene expression and metabolic activities in bacteria, with potential applications in industry and biomedicine.
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August 27, 2:29 PM
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TtgR, a transcriptional repressor from Pseudomonas putida, plays a key role in regulating multidrug resistance by controlling the expression of genes in response to various ligands. Despite its broad specificity, TtgR represents a promising candidate for the development of transcription factor (TF)-based biosensors. In this study, we utilized TtgR and its native promoter region (PttgABC) as genetic components to construct TF-based biosensors in Escherichia coli. By coupling TtgR and PttgABC with egfp, we developed a biosensor responsive to diverse flavonoids. To enhance the selectivity and specificity of the biosensor, we genetically engineered a TtgR-binding pocket. Engineered TtgR variants exhibited altered sensing profiles, enabling the development of biosensors with tailored ligand responses. Computational structural analysis and ligand docking provided insights into the interaction mechanisms between TtgR variants and flavonoids. Notably, biosensors based on wild-type TtgR and its N110F mutant were capable of quantifying resveratrol and quercetin at 0.01 mM with >90% accuracy. Although the precise molecular mechanisms involved remain unclear and further optimization is needed, the biosensors developed herein demonstrate strong potential for applications in numerous fields. This study lays the foundation for future research that could extend the utility of TtgR-based biosensors to synthetic biology, metabolic engineering, and beyond.
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August 27, 2:17 PM
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RNA interference (RNAi, also known as RNA silencing) is one of the most important plant defense responses to combat viral invasions. Although the major components of the RNAi pathway, the steps leading to viral small interference RNA (siRNA) biogenesis, and the strategies of viral counter-defense via RNAi suppressors have been well studied, the broader roles of RNAi in virus infection and seed transmission remain less thoroughly reviewed. In particular, the increasing complexity of RNAi-associated mechanisms and their integration with other biological processes have not been comprehensively summarized. Meanwhile, an increasing number of papers report on the identification of non-canonical RNAi pathways, novel host factors involved in RNAi, and the possibility of small RNAs acting cross-kingdom and modulating plant-virus-vector tritrophic interactions. In this review, we briefly overview the roles of RNAi in plant viral infections, and describe recent advances with an emphasis on the discoveries of novel positive and negative RNAi regulators, potential upstream and downstream signaling pathways of antiviral RNAi, and the prospects and challenges of double-stranded RNA applications, either expressed from transgenes or exogenously provided by a spray. We will also discuss how these novel findings reshape our views on (antiviral) RNAi, highlight remaining knowledge gaps and examine how these advances influence plant-virus co-evolution and inform the strategies that can be utilized to manage plant virus diseases to reduce their impact.
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August 27, 12:32 PM
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Genetic interactions are fundamental to the architecture of complex traits, yet the molecular mechanisms by which variant combinations influence cellular pathways remain poorly understood. Here, we answer the question of whether interactions between genetic variants can activate unique pathways and if such pathways can be targeted to modulate phenotypic outcomes. The model organism Saccharomyces cerevisiae was used to dissect how two causal SNPs, MKT189G and TAO34477C, interact to modulate metabolic and phenotypic outcomes during sporulation. By integrating time-resolved transcriptomics, absolute proteomics, and targeted metabolomics in isogenic allele replacement yeast strains, we show that the combined presence of these SNPs uniquely activates the arginine biosynthesis pathway and suppresses ribosome biogenesis, reflecting a metabolic trade-off that enhances sporulation efficiency. Functional validation demonstrates that the arginine pathway is essential for mitochondrial activity and efficient sporulation only in the double-SNP background. Our findings show how genetic variant interactions can rewire core metabolic networks, providing a mechanistic framework for understanding polygenic trait regulation and the emergence of additive effects in complex traits. The mechanisms through which variants of different genes interact to affect cell pathways remain poorly understood. Here, the authors show that combinations of two genetic variants in yeast can reprogram cellular metabolism and affect sporulation.
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August 27, 11:55 AM
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Cotton is an economically important global crop, the yield and quality of which are strongly influenced by soil nitrogen. Low nitrogen use efficiency poses an important challenge to improve cotton yield and quality. The use of arbuscular mycorrhizal fungi (AMF) has been proposed as an effective solution to this challenge. Therefore, we conducted an indoor experiment using a compartmentalized culture system with cotton as the material and established three nitrogen treatments (1 g·kg−1, 0.7 g·kg−1, and 0 g·kg−1) to investigate whether symbiosis between AMF and cotton roots could improve the nitrogen absorption capacity of cotton. Under high-nitrogen, low-nitrogen, and nitrogen- free treatments, the contributions of AMF colonization to root NO₃⁻-N and NH₄⁺-N were 5.89%, 10.10%, 19.92% and 24.35%, 12.37%, 13.16% respectively. Furthermore, the symbiosis between AMF and roots promoted the absorption of soil NO₃⁻-N, NH₄⁺ -N, and dissolved organic nitrogen, and was beneficial for increasing the content of soil readily oxidizable carbon. Additionally, AMF colonization was significantly positively correlated with root tissue density, cotton biomass, and soil microbial activity, but significantly negatively correlated with soil total organic carbon. Therefore, under nitrogen - reduction condition, roots will be more dependent on the contribution of mycelium to NO₃⁻-N, and AMF colonization was significantly positively correlated with root tissue density (P < 0.05), suggesting that mycelium may prolong its functional cycle by improving the root structure, thereby reducing the carbon and nitrogen consumption in host organ reconstruction. However, this mechanism needs to be further verified in combination with the direct measurement of root turnover rate.
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August 27, 9:59 AM
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Scientific research has revealed only a minuscule fraction of the enzymes that evolution has generated to power life’s essential chemical reactions—and an even tinier fraction of the vast universe of possible enzymes. Beyond the enzymes already annotated lie an astronomical number of biocatalysts that could enable sustainable chemical production, degrade toxic pollutants, and advance disease diagnosis and treatment. For the past few decades, directed evolution has been a powerful strategy for reshaping enzymes to access new chemical transformations: by harnessing nature’s existing diversity as a starting point and taking inspiration from nature’s most powerful design process, evolution, to modify enzymes incrementally. Recently, artificial intelligence (AI) methods have started revolutionizing how we understand and compose the language of life. In this perspective, we discuss a vision for AI-driven enzyme discovery to unveil a world of enzymes that transcends biological evolution and perhaps offers a route to genetically encoding almost any chemistry.
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genetic part