ACS Synthetic Biology最新文献

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Laccase-Based Biosensors for Functional Screening of Transcription Factors in Trichoderma reesei 漆酶生物传感器在里氏木霉转录因子功能筛选中的应用
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-23 DOI: 10.1021/acssynbio.6c00288
Ying Xia, Junjun Yu, Xia Wang, Ying Feng, Yijing Lin, Xinda Lin
{"title":"Laccase-Based Biosensors for Functional Screening of Transcription Factors in Trichoderma reesei","authors":"Ying Xia,&nbsp;Junjun Yu,&nbsp;Xia Wang,&nbsp;Ying Feng,&nbsp;Yijing Lin,&nbsp;Xinda Lin","doi":"10.1021/acssynbio.6c00288","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00288","url":null,"abstract":"<p>Efficient transcription factor (TF) screening is essential for the rational optimization of industrial microbial strains. Here, we present an absorbance-activated laccase-based biosensor (AALB) platform designed for rapid functional screening of TFs in <em>Trichoderma reesei</em>. By using laccase as a reporter, the AALB platform offers a robust and cost-effective screening system for TF functional evaluation. The secreted heterologous laccase also complements <em>T. reesei</em>’s native cellulolytic machinery, expanding its enzymatic repertoire for lignocellulosic biomass deconstruction. The core of the AALB platform is a Pcbh1-regulated laccase expression cassette, enabling sensitive and efficient selection of TF variants based on absorbance readouts. To further improve sensitivity, we introduced a quadruple repeat of the <em>cis</em>-element-dense segment in the <em>cbh1</em> promoter and integrated a high-activity heterologous laccase at the SLP1 site of the <em>T. reesei</em> genome. Following a miniaturized 2 day pre-culture in 24-well plates, the AALB platform enables TF variant ranking within 30 min of absorbance readout in 200 μL 96-well reactions, reducing the need for extended shake-flask fermentation and separate downstream enzymatic or molecular assays during the initial screen. Using AALB, we successfully identified TF variants with robust transcriptional regulation. The screening results were validated through transcript quantification of laccase and XYR1 and extracellular laccase activity assays. Notably, the XYR1 mutation XYR1_V821F, selected via AALB, significantly increased laccase transcript levels compared to PoLAC-SLP1 chassis control, with laccase activity reaching 17.74 ± 0.76 IU/mL<span></span>a 2.7-fold improvement. Further characterization of the AALB-selected XYR1_V821F strain showed increased extracellular laccase activity together with increased xylanase and filter paper activities, with extracellular xylanase and filter paper activities increased by 2.7- and 1.9-fold, respectively, and enhanced rice straw hydrolysis under the tested fermentation and hydrolysis conditions. The AALB platform provides valuable insights into the synthetic biology and metabolic engineering of <em>T. reesei</em>, facilitating the development of industrial strains for lignocellulosic biomass processing and enzyme production.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4075–4089"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optogenetically Regulated siRNA Synthesis and Outer Membrane Vesicle-Mediated Delivery by Engineered Bacteria 光基因调控的siRNA合成和工程细菌外膜囊泡介导的递送
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-02 DOI: 10.1021/acssynbio.6c00293
Long Li, Xin Huang, Xiaoyu Dong, Yanle Wang, Yanning Zhang, Guijie Bai, Yue Jiang, Le Liu, Yinuo Qiu, Zhijie Feng, Peiyuan Liu, Duo Liu, Si Lin, Chenguang Hu, Peiqi Zhao, Dawei Sun, Yanyan Shi, Hanjie Wang
{"title":"Optogenetically Regulated siRNA Synthesis and Outer Membrane Vesicle-Mediated Delivery by Engineered Bacteria","authors":"Long Li,&nbsp;Xin Huang,&nbsp;Xiaoyu Dong,&nbsp;Yanle Wang,&nbsp;Yanning Zhang,&nbsp;Guijie Bai,&nbsp;Yue Jiang,&nbsp;Le Liu,&nbsp;Yinuo Qiu,&nbsp;Zhijie Feng,&nbsp;Peiyuan Liu,&nbsp;Duo Liu,&nbsp;Si Lin,&nbsp;Chenguang Hu,&nbsp;Peiqi Zhao,&nbsp;Dawei Sun,&nbsp;Yanyan Shi,&nbsp;Hanjie Wang","doi":"10.1021/acssynbio.6c00293","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00293","url":null,"abstract":"<p>Outer membrane vesicles (OMVs), as promising delivery vectors, have been extensively explored for the delivery of nucleic acid-based drugs, particularly the RNA therapy. However, RNA-loaded OMVs delivery systems derived from in vivo engineered bacteria lack the controllable way for regulating target RNA synthesis. Constitutive RNA synthesis may not only exert excessive metabolic burden on engineered bacteria but also lead to unexpected RNA package and delivery, markedly compromising in vivo biomedical applications. Herein, we developed an optogenetically regulated small interfering RNA (siRNA) synthesis and delivery system based on engineered bacterial OMVs. A proof of concept was demonstrated for combining this optogenetic siRNA delivery system with photothermal therapy (PTT) to evaluate tumor thermal resistance modulation by using dual functional engineered strains. The first strain (opto-siTRPV1@OMVs BL-ves) was designed to secrete siRNA targeting transient receptor potential vanilloid subtype 1 (TRPV1) in response to green light stimulation, while a second melanin-producing strain (BL21-TYR) was established for efficient photothermal ablation under 808 nm near-infrared (NIR) laser irradiation. Experimental results showed that the combined therapeutic regimen demonstrated a preliminary tumor growth inhibition rate of approximately 63.06% in a murine model. Furthermore, this regimen remodeled the immunosuppressive tumor microenvironment (TME), activated antigen-presenting cells, promoted the infiltration of effector T cells, and thereby triggered robust anti-tumor immune responses. This study presents a novel strategy for the precise and regulated delivery of siRNA, and demonstrates the feasibility of optogenetically controlled siRNA production and OMV-mediated delivery in a laboratory setting.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4099–4111"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction to “Phosphoserine as an Alternative Energy Source for E. coli Cell-Free Protein Synthesis with Increased Yield and Prolonged Activity” 更正“磷酸丝氨酸作为大肠杆菌无细胞蛋白合成的替代能源,产量增加,活性延长”
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-17 DOI: 10.1021/acssynbio.6c00670
Shanny Ackerman, Yael Fink, Yasmin Habib, Devora Cohen-Karni, Omer Adir, Gal Chen, Yuval Richtman, Sónia Siquenique, Michael Levy, Jeny Shklover, Bruno Sarmento, Avi Schroeder
{"title":"Correction to “Phosphoserine as an Alternative Energy Source for E. coli Cell-Free Protein Synthesis with Increased Yield and Prolonged Activity”","authors":"Shanny Ackerman,&nbsp;Yael Fink,&nbsp;Yasmin Habib,&nbsp;Devora Cohen-Karni,&nbsp;Omer Adir,&nbsp;Gal Chen,&nbsp;Yuval Richtman,&nbsp;Sónia Siquenique,&nbsp;Michael Levy,&nbsp;Jeny Shklover,&nbsp;Bruno Sarmento,&nbsp;Avi Schroeder","doi":"10.1021/acssynbio.6c00670","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00670","url":null,"abstract":"","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4381–4381"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Balancing Precursor Supply and Enhancing Enzyme Solubility for Efficient Production of (S)-Reticuline in Escherichia coli 平衡前体供应和提高酶溶解度对大肠杆菌高效生产(S)-网状氨酸的影响
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-23 DOI: 10.1021/acssynbio.6c00417
Xiaxia Zhang, Muhammad Hassan Butt, Wen Zhang, Yuan Gao, Shibo Guo, Jianfeng Fang, Xiaolin Shen, Jia Wang, Xinxiao Sun, Qipeng Yuan
{"title":"Balancing Precursor Supply and Enhancing Enzyme Solubility for Efficient Production of (S)-Reticuline in Escherichia coli","authors":"Xiaxia Zhang,&nbsp;Muhammad Hassan Butt,&nbsp;Wen Zhang,&nbsp;Yuan Gao,&nbsp;Shibo Guo,&nbsp;Jianfeng Fang,&nbsp;Xiaolin Shen,&nbsp;Jia Wang,&nbsp;Xinxiao Sun,&nbsp;Qipeng Yuan","doi":"10.1021/acssynbio.6c00417","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00417","url":null,"abstract":"<p>Benzylisoquinoline alkaloids (BIAs) are pharmacologically valuable natural products, yet their microbial production in <em>Escherichia coli</em> is hindered by two major bottlenecks: (1) imbalanced metabolic flux between the two upstream precursors, 3,4-dihydroxyphenylacetaldehyde (3,4-DHPAA) and dopamine, and (2) poor soluble expression of plant-derived enzymes, particularly norcoclaurine synthase (NCS) and the methyltransferase Ps4′OMT2. To address these challenges, we systematically engineered <em>E. coli</em> for efficient synthesis of (<em>S</em>)-reticuline, the universal precursor to diverse BIAs. First, to resolve the flux imbalance, we introduced a heterologous ω-transaminase (ω-TA) that dynamically interconverts 3,4-DHPAA and dopamine, thereby coordinating precursor supply without tedious tuning of branch pathways. Second, to overcome enzyme insolubility, we combined solubility-enhancing strategies<span></span>including SUMO fusion, ProteinMPNN-guided design, and N-terminal truncation<span></span>which markedly improved the soluble expression of CjNCS and Ps4′OMT2. Furthermore, strengthening the <em>S</em>-adenosylmethionine (SAM) regeneration cycle through integration of <em>luxS</em>, <em>mtn</em>, and <em>metF</em> genes enhanced the efficiency of the three sequential methylation reactions. The final engineered strain achieved a (<em>S</em>)-reticuline titer of 347 mg/L in shake-flask fermentation. Overall, this work establishes an efficient <em>E. coli</em> chassis for sustainable BIAs production by systematically tackling flux imbalance and enzyme solubility.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4229–4239"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mining Phage Genomes for Regulatory Elements to Develop a SynBio Toolbox for Non-Model Pseudomonads 挖掘噬菌体基因组的调控元件,开发非模型假单胞菌的合成生物工具箱
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-23 DOI: 10.1021/acssynbio.6c00389
Jorien Poppeliers, Maarten Boon, Alison Kerremens, Rob Lavigne
{"title":"Mining Phage Genomes for Regulatory Elements to Develop a SynBio Toolbox for Non-Model Pseudomonads","authors":"Jorien Poppeliers,&nbsp;Maarten Boon,&nbsp;Alison Kerremens,&nbsp;Rob Lavigne","doi":"10.1021/acssynbio.6c00389","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00389","url":null,"abstract":"<p>Bacteriophages represent a largely untapped reservoir of regulatory elements that can expand the genetic toolbox for engineering non-model hosts. Using ONT-cappable-sequencing, we mapped full-length primary transcripts across five <em>Pseudomonas</em> phages and identified 232 transcription start sites (TSSs) and 176 transcription termination sites (TTSs), including 38 intrinsic factor-independent terminators. Motif discovery revealed 59 σ70-like promoters in KIL5, 37 in KIL3b, and unique phage-encoded RNA polymerase (RNAP) promoter motifs for KNP, ϕ2, and pphageB21, enabling discrimination between host- and phage-dependent transcriptional control. To validate these identifications, a subset of ten promoters and five terminators was quantitatively characterized in vivo in <em>Pseudomonas fluorescens</em> strain GL-S-306, showing promoter activities spanning a large dynamic range and terminator efficiencies allowing complete transcriptional termination. These data establish the first experimentally validated, phage-derived library of promoters and terminators for <em>P. fluorescens</em> and <em>Pseudomonas syringae</em>, providing chassis-specific regulatory parts that enable more finetuned gene-expression than current cross-species SynBio tools. Our results position phage transcriptomics as a scalable strategy for mining regulatory elements tailored to non-model bacterial hosts, while also supporting phage design and engineering efforts and accelerating the development of new synthetic biology platforms.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4207–4216"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Designing a DeepPCD Strategy for Efficient Engineering Nitrilases toward Industrial Bioconversion 面向工业生物转化的高效工程硝化酶的深度ppcd策略设计
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-10-03 DOI: 10.1021/acssynbio.6c00038
Xiao-Ting Zhou, Qian Guo, Yao-Fang Ding, Qi Shen, Qi Shen, Ya-Ping Xue, Yu-Guo Zheng
{"title":"Designing a DeepPCD Strategy for Efficient Engineering Nitrilases toward Industrial Bioconversion","authors":"Xiao-Ting Zhou,&nbsp;Qian Guo,&nbsp;Yao-Fang Ding,&nbsp;Qi Shen,&nbsp;Qi Shen,&nbsp;Ya-Ping Xue,&nbsp;Yu-Guo Zheng","doi":"10.1021/acssynbio.6c00038","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00038","url":null,"abstract":"<p>The integration of artificial intelligence with protein engineering has created unprecedented opportunities for enzyme discovery and the enhancement of overall catalytic performance. In this study, a novel nitrilase, <em>Bh</em>NIT, was identified from <em>Bradyrhizobium</em><em>huanghuaihaiense</em> through a computationally assisted screening strategy. Using <em>Bh</em>NIT as the target protein for engineering, we established DeepPCD as an integrated computationally guided workflow that organizes sequence-design, structure-filtering, stability-assessment, evolutionary-compatibility, and molecular dynamics analyses to prioritize experimentally testable mutations. Compared with approaches that require extensive experimental screening of large mutant libraries, the DeepPCD workflow facilitates efficient enzyme engineering modifications. By modifying only seven candidate residues of <em>Bh</em>NIT, we obtained a mutant exhibiting a 1.3 × 10<sup>5</sup>-fold improvement in hydrolytic efficiency. In addition, this mutant showed a 20.4°C increase in melting temperature and a broader operational pH range extending toward more alkaline conditions, substantially enhancing its potential for industrial applications. Molecular dynamics simulations and structural analysis revealed that the enhanced performance stems from effective reshaping of the substrate-binding pocket and access channel, along with a strengthened interaction network. Furthermore, preliminary computational application to additional nitrilases suggested the potential transferability of this workflow within the nitrilase family. Overall, this work provides an experimentally validated case study for computationally guided nitrilase engineering and offers a practical workflow for prioritizing mutations that may improve activity and stability, although broader generalization will require further validation across more diverse enzyme systems.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4007–4022"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149211003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep Learning in Enzyme Function Prediction and Novel Enzyme Discovery 酶功能预测中的深度学习和新酶的发现
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-04 DOI: 10.1021/acssynbio.6c00633
Rongsheng Gao, Youmeng Liu, Chengye Duan, Nan Qin, Kunyu Liu, Tatsuhisa Tsuboi, Zhen Chen
{"title":"Deep Learning in Enzyme Function Prediction and Novel Enzyme Discovery","authors":"Rongsheng Gao,&nbsp;Youmeng Liu,&nbsp;Chengye Duan,&nbsp;Nan Qin,&nbsp;Kunyu Liu,&nbsp;Tatsuhisa Tsuboi,&nbsp;Zhen Chen","doi":"10.1021/acssynbio.6c00633","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00633","url":null,"abstract":"<p>The rapid growth of genomic and metagenomic data has created a large gap between protein sequence discovery and enzyme functional characterization. Deep learning has become an important tool for enzyme-related prediction tasks, including EC and GO annotation, substrate specificity, catalytic-residue identification, kinetic-parameter estimation, thermostability, pH optima, and candidate discovery. This review summarizes recent progress with an emphasis on benchmark design rather than reported scores alone. We compare representative methods by input modality, training data, split strategy, leakage control, evaluation metric, and validation evidence. Across tasks, apparent performance gains can arise from dataset scale, annotation quality, homolog overlap, negative sampling, or endpoint definition rather than architecture alone. Current models are valuable for annotation and candidate prioritization, but robust discovery of remote homologs, rare functions, or new catalytic activities still requires low-identity or out-of-distribution evaluation and experimental validation.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"3937–3958"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PhAGE Enables One-Step Genome Integration of Large DNA Fragments in Escherichia coli 噬菌体使大肠杆菌中大DNA片段的一步基因组整合成为可能
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-25 DOI: 10.1021/acssynbio.6c00489
Shingo Nozaki, Yoshihiro Miwa
{"title":"PhAGE Enables One-Step Genome Integration of Large DNA Fragments in Escherichia coli","authors":"Shingo Nozaki,&nbsp;Yoshihiro Miwa","doi":"10.1021/acssynbio.6c00489","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00489","url":null,"abstract":"<p><em>Escherichia coli</em> is a well-established model organism in molecular biology and biotechnology. Despite its long history as a laboratory workhorse, the efficient single-step chromosomal integration of large DNA fragments remains a challenge. Currently known methods are either simple but have limitations on insert size, or flexible but laborious requiring plasmid construction or multi-step procedures. Here, we present PhAGE (<span>Ph</span>age-<span>A</span>ssisted <span>G</span>enome <span>E</span>ngineering), which enables the integration of ∼20 kb DNA fragments into the <em>E. coli</em> genome within a single day. PhAGE method uses in vitro packaging of recombinant DNA into bacteriophage capsids, followed by general transduction to introduce pre-assembled DNA with flanking homology arms into recipient cells. This approach allows efficient and landing pad-free integration of large constructs into the target loci. We demonstrate its usefulness through rapid integration of multi-gene operons. PhAGE resolves the long-standing trade-off between simplicity and insert size in <em>E. coli</em> genome engineering, providing a powerful assembly-to-integration toolkit that accelerates strain construction across a wide range of applications, from biosynthetic pathway engineering to genome-scale design.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4266–4275"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Meeting Proceedings from the 5th Minimal Cell WorkshopLife at Its Simplest Foundations in Minimal Cells 第五届最小细胞研讨会会议记录:最小细胞中最简单的生命基础
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-25 DOI: 10.1021/acssynbio.6c00454
Zumra Peksaglam Seidel, Mariana Mathias Conroy Araujo, Hajar Estiri, Ronald Rodriguez, John I. Glass
{"title":"Meeting Proceedings from the 5th Minimal Cell WorkshopLife at Its Simplest Foundations in Minimal Cells","authors":"Zumra Peksaglam Seidel,&nbsp;Mariana Mathias Conroy Araujo,&nbsp;Hajar Estiri,&nbsp;Ronald Rodriguez,&nbsp;John I. Glass","doi":"10.1021/acssynbio.6c00454","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00454","url":null,"abstract":"<p>The fifth annual virtual minimal cell workshop, hosted by the J. Craig Venter Institute (JCVI), brought together an international community of researchers from academic, industrial, and government laboratories. The 2025 meeting featured 30 talks focused on using minimal bacterial cells to probe the fundamental principles of life, develop new construction strategies, and advance predictive frameworks for cellular behavior. Most of the presentations centered on the JCVI minimal bacterial cells JCVI-syn3.0, JCVI-syn3A, and JCVI-syn3B. Multiple talks addressed the persistent set of essential genes with unknown or partially defined functions, leveraging advanced imaging, computational modeling, and experimental evolution to uncover their cellular roles. Studies of protein moonlighting, membrane biophysics, cell division, metabolism, and aging demonstrated how minimal cells expose fundamental biological constraints often obscured in more complex organisms. Whole-cell computational models increasingly reproduce growth, division, metabolism, gene regulation, and macromolecular assembly. Presentations also highlighted new approaches to whole-genome transplantation, development of alternative minimal genome chassis, synthetic cell assembly from non-living components, chromosome-scale minimization in eukaryotes, and conceptual agricultural and prebiotic systems. Collectively, these efforts position minimal cells as powerful platforms for understanding, building, and predicting living systems.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"3929–3936"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149211001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Automated Mini-Bioreactors Reveal the Temporal Dynamics and Multi-Omics Responses of CRISPRi Knockdowns in Pseudomonas putida 自动微型生物反应器揭示恶臭假单胞菌CRISPRi敲低的时间动态和多组学响应
IF 4.5 2区 生物学
ACS Synthetic Biology Pub Date : 2026-10-16 Epub Date: 2026-09-18 DOI: 10.1021/acssynbio.6c00205
Mariana Arango Saavedra, Sara Grassi, Magnus Ganer Jespersen, Catarina Rocha, Viji Kandasamy, Lars Keld Nielsen, Pablo Ivan Nikel, Stefano Donati
{"title":"Automated Mini-Bioreactors Reveal the Temporal Dynamics and Multi-Omics Responses of CRISPRi Knockdowns in Pseudomonas putida","authors":"Mariana Arango Saavedra,&nbsp;Sara Grassi,&nbsp;Magnus Ganer Jespersen,&nbsp;Catarina Rocha,&nbsp;Viji Kandasamy,&nbsp;Lars Keld Nielsen,&nbsp;Pablo Ivan Nikel,&nbsp;Stefano Donati","doi":"10.1021/acssynbio.6c00205","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00205","url":null,"abstract":"<p>Characterizing CRISPR interference (CRISPRi) phenotypes presents a fundamental temporal challenge: pre-existing overabundance of target proteins can mask early silencing, requiring extended growth for dilution, yet prolonged repression rapidly selects for escaper mutants. To resolve this, we integrated a tightly regulated CRISPRi system in <em>Pseudomonas putida</em> with an automated mini bioreactor platform operating in turbidostat mode. By maintaining continuous exponential growth, we mapped the exact temporal dynamics of essential gene silencing. We identified a critical observation window between 7.8 and 26.7 h (corresponding to 6.4−23.5 cumulative cell doublings of the uninduced condition) where repression exerts its maximum physiological impact, directly preceding population takeover by target-site mutated escapers. Applying this workflow to the arginine biosynthesis pathway, multi-omics profiling disentangled transient physiological buffering from long-term mutational events, revealing that <em>argH</em> and <em>argG</em> knockdowns trigger highly diverse metabolomic perturbations. This scalable framework overcomes batch culture limitations for CRISPRi experiments, ensuring precise temporal control for accurate phenotypic characterization and reliable functional genomics.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 10","pages":"4023–4038"},"PeriodicalIF":4.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149210940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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