ACS Synthetic Biology最新文献_第6页

Engineering DNA-Targeting CRISPR and CRISPR-Like Effectors: Advances from Rational Design and High-Throughput Screening to AI-Driven Development 工程dna靶向CRISPR和CRISPR样效应物：从理性设计和高通量筛选到人工智能驱动开发的进展

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-12 DOI: 10.1021/acssynbio.6c00386

Lingwei She, Zeyu Liang, Qin Zou, Yi-Xin Huo

{"title":"Engineering DNA-Targeting CRISPR and CRISPR-Like Effectors: Advances from Rational Design and High-Throughput Screening to AI-Driven Development","authors":"Lingwei She, Zeyu Liang, Qin Zou, Yi-Xin Huo","doi":"10.1021/acssynbio.6c00386","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00386","url":null,"abstract":"Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute adaptive immune systems in prokaryotes and have transformed life sciences, precision medicine, and synthetic biology as programmable genome-editing tools. Despite their broad utility, naturally occurring DNA-targeting Cas effectors remain constrained by several intrinsic limitations, including large protein size that complicates delivery, stringent protospacer adjacent motif (PAM) requirements that restrict targetable genomic space, and mismatch tolerance that can lead to off-target activity and potential genotoxicity. These challenges have made Cas protein engineering and the discovery of novel CRISPR and CRISPR-like systems from metagenomic resources central to the development of next-generation genome-editing platforms. This Review places recent advances within an integrated synthetic biology engineering continuum that links natural effector discovery, structure-guided hypothesis generation, high-throughput functional screening, machine learning-enabled model construction, and iterative redesign. This Review summarizes progress in the screening, optimization, and functional engineering of DNA-targeting CRISPR and CRISPR-like effectors, with emphasis on structure-guided rational design, directed evolution coupled with high-throughput screening, bioinformatics- and evolution-guided mining of novel systems from large-scale sequence databases, and artificial intelligence-assisted development. By integrating these strategies, we highlight how CRISPR effector engineering is moving toward design-build-test-learn (DBTL)-inspired workflows that expand the functional landscape of genome-editing technologies and advance genome editing toward improved efficiency, safety, and programmability.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3518–3542"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003701","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

DeepCRISPR-Typer: Accurate CRISPR-Cas Identification and Subtyping in Metagenomes via Integrated Deep Learning DeepCRISPR-Typer：通过集成深度学习在宏基因组中准确识别CRISPR-Cas并分型

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-12 DOI: 10.1021/acssynbio.6c00398

Long Wen, Minghui Jing, Yanyan Li, Xuequn Shang, Xingyu Liao

{"title":"DeepCRISPR-Typer: Accurate CRISPR-Cas Identification and Subtyping in Metagenomes via Integrated Deep Learning","authors":"Long Wen, Minghui Jing, Yanyan Li, Xuequn Shang, Xingyu Liao","doi":"10.1021/acssynbio.6c00398","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00398","url":null,"abstract":"Accurate identification and classification of CRISPR-Cas systems are crucial for understanding microbial immune mechanisms and developing novel genome-editing tools. However, traditional homology-based mining methods face severe computational bottlenecks and assembly fragmentation challenges when processing massive metagenomic data. Here, we present DeepCRISPR-Typer, a comprehensive computational framework integrating a large protein language model (TEMC-Cas), a deep sequence feature extractor (CRISPR-RepTyper), and an adaptive targeted HMM profiling strategy. DeepCRISPR-Typer integrates array and Cas evidence and significantly reduces computational overhead by dynamically invoking subtype-specific HMM subsets. In metagenomic dataset evaluations, DeepCRISPR-Typer achieved a classification accuracy of 94.26% and demonstrated a significant acceleration of approximately 1 orders of magnitude compared to existing mainstream tools. This research provides a robust and scalable engine for metagenome-scale CRISPR system discovery, significantly expanding the mining toolbox for genome engineering applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3738–3749"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003703","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

Directed Evolution of an Escherichia coli Secretor Strain Using the Curli Pathway 利用Curli途径定向进化大肠杆菌分泌菌株

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-13 DOI: 10.1021/acssynbio.6c00050

Anton Kan, Sivaram Subaya Emani, Neel S. Joshi

{"title":"Directed Evolution of an Escherichia coli Secretor Strain Using the Curli Pathway","authors":"Anton Kan, Sivaram Subaya Emani, Neel S. Joshi","doi":"10.1021/acssynbio.6c00050","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00050","url":null,"abstract":"A key goal of many bacterial engineering projects is to produce protein, due to their potent chemical and material functions. However, recombinant proteins are usually produced intracellularly, and secreting arbitrary proteins directly into an extracellular environment is challenging. In this work, we explored recombinant protein secretion using the curli secretion pathway in the probiotic Escherichia coli Nissle 1917 strain (EcN). We developed a Green Fluorescent Protein (GFP) secretion system by fusing GFP of the N-terminus sequence from the curli monomer protein while co-expressing the curli export machinery. We characterized and optimized our designs, obtaining ∼60 μg/mL extracellular GFP protein from plasmid pSecGFP1h. To further increase protein yield, we performed a directed evolutionary process using chemical mutagenesis and selecting for both high GFP yield and secretion of a protein toxic to E. coli. We performed several rounds of mutagenesis and selection to generate two distinct lineages, which both secreted ∼120 μg/mL extracellular GFP. We then sequenced and analyzed the genomes of strains making up the two lineages, assembling genome sequences for 8 EcN-derived strains, finding ∼50 point mutations per round of mutagenesis, and identifying the genes affected. We further assessed the capability of our evolved E. coli strains to secrete diverse proteins, including proteinaceous materials, enzymes, and therapeutic peptides. We obtained successful secretion for many proteins and found that secretion was sequence-specific, although no simple metric could predict success. The methodology we developed for microbial strain engineering and protein secretion has the potential to be generalizable to many biotechnological applications to take advantage of the abilities of proteins.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3593–3606"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003739","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

Reprogramming Komagataella phaffii Cell Factory for High-Yield Production of 3S,3′S-Astaxanthin via Multiplex Metabolic Engineering and Its Application 多重代谢工程重编程法菲Komagataella phaffii细胞工厂高产3S， 3S -虾青素及其应用

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-17 DOI: 10.1021/acssynbio.6c00238

Xinying Zhang, Jiyuan Hu, Yanxuan Wu, Yue Huang, Junxi Chen, Shuli Liang, Ying Lin

{"title":"Reprogramming Komagataella phaffii Cell Factory for High-Yield Production of 3S,3′S-Astaxanthin via Multiplex Metabolic Engineering and Its Application","authors":"Xinying Zhang, Jiyuan Hu, Yanxuan Wu, Yue Huang, Junxi Chen, Shuli Liang, Ying Lin","doi":"10.1021/acssynbio.6c00238","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00238","url":null,"abstract":"Astaxanthin is a keto-carotenoid with high added value. In this study, we aimed to biosynthesize 3S,3′S-astaxanthin efficiently and sustainably from the renewable single-carbon (C1) feedstock methanol through multiplex metabolic engineering strategies in Komagataella phaffii. First, the K. phaffii cell-free terpene synthesis system was established successfully and applied to evaluate the astaxanthin synthase combinations rapidly. We then systematically engineered K. phaffii for the overproduction of 3S,3′S-astaxanthin from methanol by tuning the carotenoid synthesis module rationally, optimizing the precursor supply and carotenoid storage globally, thereby achieving a significant elevation in astaxanthin content from 3.910 mg/g to 7.513 mg/g. Thereafter, key node enzyme assembly, branch route reconstruction, and cofactor engineering were employed to further improve astaxanthin accumulation, achieving a significant increase of astaxanthin content to 11.397 mg/g. Finally, the astaxanthin production reached 4.75g/L under fed-batch fermentation, which is the highest astaxanthin level reported in an engineered microbe to date. In addition, the synthesized astaxanthin was successfully and effectively applied in shrimp farming for color enhancement and antioxidant effects. These results demonstrate the potential of K. phaffii as a promising platform for sustainable green production of value-added terpenoid compounds from organic one-carbon feedstocks and will pave the way for astaxanthin industrial production.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3632–3644"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003748","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

Boosted Cell-Free Gene Expression for Robust Signal Readout from a Single-Copy DNA Template in Microdroplets 微滴中单拷贝DNA模板增强无细胞基因表达的鲁棒信号读出

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-27 DOI: 10.1021/acssynbio.6c00471

Taro Furubayashi, Naohiro Terasaka, Kenya Tajima, Hiroyuki Noji

{"title":"Boosted Cell-Free Gene Expression for Robust Signal Readout from a Single-Copy DNA Template in Microdroplets","authors":"Taro Furubayashi, Naohiro Terasaka, Kenya Tajima, Hiroyuki Noji","doi":"10.1021/acssynbio.6c00471","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00471","url":null,"abstract":"Cell-free gene expression in microcompartments constitutes a chassis for biotechnology and synthetic biology. Protein synthesis from low DNA concentrations, including a single copy per compartment, is essential for in vitro evolution of biomolecules and synthetic cells. However, insufficient protein yields from typically subpicomolar DNA inputs result in undetectable signals or inadequate activity of desired protein functions. Here we identify and largely mitigate yield-limiting bottlenecks of reconstituted in vitro transcription and translation (IVTT) at low DNA input. Systematic comparison of commercial reconstituted IVTT kits revealed that gene expression becomes limited by mRNA scarcity within the 20−200 pM DNA-input range. We further uncovered that the standard ribosome concentration is excessive at low-DNA input and shortens the lifetime of translation. These findings led to a simple optimization recipe that combines supplementation with a commercial highly active T7 RNA polymerase reagent and a reduction in ribosome concentration, which synergistically amplified gene expression by ∼10-fold across diverse fluorescent proteins and enzymes. This low-DNA-optimized formulation in picoliter droplets achieved ∼94 nM protein expression from a single copy of a PCR-derived linear DNA template (∼0.12 pM). The user-friendly boosted IVTT protocol paves the way for straightforward functional screening and in vitro reconstitution of cellular functions in DNA-scarce environments.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3784–3794"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003691","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

Engineering Novel Polyhydroxyalkanoates Using Polyketide Synthases in Pseudomonas putida 在恶臭假单胞菌中利用聚酮合成酶的工程新型聚羟基烷酸酯

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-28 DOI: 10.1021/acssynbio.6c00363

Leah S. Keiser, Aalini Jain, Panarai Primrose Gatenil, Matthias Schmidt, Yolanda Zhu, Cholapat Varongchayakul, Amarrah Crysti Len, Kyrellos Ibrahim, Elias Englund, Jay D. Keasling

{"title":"Engineering Novel Polyhydroxyalkanoates Using Polyketide Synthases in Pseudomonas putida","authors":"Leah S. Keiser, Aalini Jain, Panarai Primrose Gatenil, Matthias Schmidt, Yolanda Zhu, Cholapat Varongchayakul, Amarrah Crysti Len, Kyrellos Ibrahim, Elias Englund, Jay D. Keasling","doi":"10.1021/acssynbio.6c00363","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00363","url":null,"abstract":"Polyhydroxyalkanoates (PHAs) are bio-based polyesters with the potential to replace petroleum-based products. However, their thermal and mechanical properties are limited by the composition of the monomers used to make them. Current approaches to expanding monomer diversity require individualized pathway engineering for each targeted monomer, limiting the scalability of PHA design. In this work, we establish polyketide synthases (PKSs) as a modular and programmable platform for expanding PHA monomer diversity with variable chain length and branching. Using Pseudomonas putidaas a host, we integrate four engineered PKSs and their variants with heterologous CoA-activating enzymes and short-chain-length PHA polymerases to produce diverse (R)-3-hydroxyacid monomers with defined substitution and branching at the ɑ- and β-positions and enable their in vivo polymerization. We also apply active learning-assisted directed evolution to improve the heterodimeric PHA polymerase CapPhaEC, achieving a 3.6-fold increase in incorporation of α-branched monomers. Leveraging the modularity of PKSs, we demonstrate the biosynthesis and polymerization of linear, branched, and aromatic monomers by exchanging acyltransferase (AT) and ketoreductase (KR) domains to control chain length, branching, and stereochemistry. This study illustrates the utility of using a flexible, programmable PKS platform for rapidly designing and testing new-to-nature PHAs.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3712–3726"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003692","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

A Novel, Simple, and Highly Efficient Dual-sgRNA CRISPR/Cas9-Based Editing System in the Filamentous Fungus Fusarium oxysporum 一种新颖、简单、高效的基于双sgrna CRISPR/ cas9的丝状真菌尖孢镰刀菌编辑系统

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-12 DOI: 10.1021/acssynbio.6c00299

Wangjie Zhu, Jiaoqun Liao, Yuanyuan Liu, Huawei Zhang

{"title":"A Novel, Simple, and Highly Efficient Dual-sgRNA CRISPR/Cas9-Based Editing System in the Filamentous Fungus Fusarium oxysporum","authors":"Wangjie Zhu, Jiaoqun Liao, Yuanyuan Liu, Huawei Zhang","doi":"10.1021/acssynbio.6c00299","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00299","url":null,"abstract":"Fusarium oxysporum, as one of the most common filamentous fungi, possesses great biosynthetic potential for natural products. However, the lack of efficient genetic tools has hindered functional genome mining and metabolic engineering in this fungus. In this study, a novel highly efficient CRISPR/Cas9-based dual-sgRNA expression editing system for F. oxysporum was successfully developed through construction of a robust plasmid platform pFRCas9-G418 using incorporation of an endogenous histone H2B nuclear localization signal and a 5S rRNA promoter-driven polycistronic tRNA−sgRNA cassette. This system is suitable not only for single-gene editing but also for large-fragment deletion and multiplex gene editing, although the editing efficiency is somewhat lower. First, this new CRISPR/Cas9 system exhibited a high efficiency of 93.75% ± 6.25% for deletion of the Fusarium cyclin C1 (fcc1) gene (∼1 kb), which was usually selected as the target gene responsible for yellow pigment accumulation. Then, knockout of the core NRPS gene sanB (∼19 kb) and knock-in of the strong promoter gpdA in the N-methylsansalvamide (SA) biosynthetic gene cluster (BGC) in strain F. oxysporum R1 using this system, respectively, led to no SA yield and an increase of 26.4% SA titer, confirming its capacity for large gene deletion and gene knock-in. Furthermore, one-step dual-gene knockout of hat1 (histone acetyltransferase gene, ∼1.5 kb) and pacC (pH-responsive transcription factor, ∼2 kb) was first achieved in Fusarium species. This versatile platform provides a powerful tool for editing gene(s) of various sizes in F. oxysporum.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3676–3685"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003700","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

IHLO-DTI: Drug-Target Interaction Prediction Based on Improved Hypergraph Neural Network and Laplacian Matrix Optimization 基于改进超图神经网络和拉普拉斯矩阵优化的药物-靶标相互作用预测

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-12 DOI: 10.1021/acssynbio.6c00326

Guolongwei Dai, Tao Luo, Dandan Li, Zeping Liu, Jiaying Gu, Lingjie Fan, Tao Lin, Quan Wei, Fengyi Wang

{"title":"IHLO-DTI: Drug-Target Interaction Prediction Based on Improved Hypergraph Neural Network and Laplacian Matrix Optimization","authors":"Guolongwei Dai, Tao Luo, Dandan Li, Zeping Liu, Jiaying Gu, Lingjie Fan, Tao Lin, Quan Wei, Fengyi Wang","doi":"10.1021/acssynbio.6c00326","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00326","url":null,"abstract":"Accurate prediction of drug-target interactions is pivotal for accelerating drug discovery and drug repurposing. However, existing advanced methods often fail to effectively characterize the many-to-many interactions between drugs and targets. Furthermore, they struggle to fully mine the structural features of drugs and proteins. To address these limitations, we propose IHLO-DTI, a novel prediction model based on an improved hypergraph neural network and Laplacian matrix optimization. First, we construct drug, protein, and drug−protein pair hypergraphs, where shared-drug and shared-target relationships are used to characterize multi-target activity and shared-target regulation. We then optimize hyperedge weights using a Laplacian matrix to enhance biologically meaningful high-order associations and suppress potential noise. Second, we use simplified graph convolution and graph convolutional network to extract global and local features, enabling efficient modeling of multi-level semantic information for drugs and targets. Next, we introduce a cross-attention mechanism and a dynamic gating module to perform fine-grained fusion of multi-channel features, improving the representation of cross-modal information interactions. Finally, we jointly train the model with contrastive learning and cross-entropy loss to enhance the consistency and discriminability of the learned representations. IHLO-DTI achieves mean AUROC and AUPR values of 0.9777 and 0.9716, respectively, on two public datasets. IHLO-DTI can effectively capture high-order many-to-many interactions between drugs and targets, improving prediction accuracy and robustness. It provides a more reliable computational tool for clinical drug screening, repurposing, and precision medicine research.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3686–3701"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003734","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

Biofoundry Architect 1.0: A Robot-Assisted Module Configurator and Workflow Designer with Hub Interoperability and Throughput-Workflow Economic Evaluation 生物铸造厂架构师1.0：机器人辅助模块配置器和工作流设计器，具有集线器互操作性和吞吐量-工作流经济评估

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-20 DOI: 10.1021/acssynbio.6c00456

Jun Sung Park, Yu Been Heo, Han Min Woo

{"title":"Biofoundry Architect 1.0: A Robot-Assisted Module Configurator and Workflow Designer with Hub Interoperability and Throughput-Workflow Economic Evaluation","authors":"Jun Sung Park, Yu Been Heo, Han Min Woo","doi":"10.1021/acssynbio.6c00456","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00456","url":null,"abstract":"Laboratory automation has rapidly advanced across chemistry, materials science, and the life sciences, enabling high-throughput and predictive experimentation. In synthetic biology, biofoundries facilitate Design−Build−Test−Learn cycles through automated workflows but remain limited by software tools lacking integration and throughput-workflow economic evaluation. Here, we present Biofoundry Architect 1.0, an open, web-based platform for designing, evaluating, and comparing automated workflows using robot-assisted modules (RAMs). The system enables quantitative assessment of performance metrics, including the turnaround time and cost, while ensuring workflow compatibility and scalability. By supporting modular design, interoperability, and community-based sharing of workflows, Biofoundry Architect bridges the gap between planning and execution, improving efficiency, accessibility, and collaborative innovation in laboratory automation. This web-based Biofoundry Architect software can be viewed at https://biofoundry-architect.streamlit.app/, and all code is released under the license GNU General Public License version 3.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3866–3871"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003778","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

Paving the Way for a Minimal CHO ChassisExploring the Upper Limits of Megabase-Scale Deletions through DNA Repair Modulation 为最小的CHO底盘铺平道路通过DNA修复调制探索超大规模缺失的上限

IF 4.5 2区生物学

ACS Synthetic Biology Pub Date : 2026-09-18 Epub Date: 2026-08-07 DOI: 10.1021/acssynbio.6c00460

Melina Bräuer, Emely Walker, Stefan Schneider, Linus Weiß, Anna Geiger, Benjamin Lindner, Oliver Hädicke, Moritz Schmidt, Simon Fischer, Kerstin Otte

{"title":"Paving the Way for a Minimal CHO ChassisExploring the Upper Limits of Megabase-Scale Deletions through DNA Repair Modulation","authors":"Melina Bräuer, Emely Walker, Stefan Schneider, Linus Weiß, Anna Geiger, Benjamin Lindner, Oliver Hädicke, Moritz Schmidt, Simon Fischer, Kerstin Otte","doi":"10.1021/acssynbio.6c00460","DOIUrl":"https://doi.org/10.1021/acssynbio.6c00460","url":null,"abstract":"Chinese hamster ovary (CHO) cells are the predominant mammalian host for therapeutic protein production, yet their large genome contains substantial non-essential DNA that may impose metabolic burden and contribute to process variability. Here, we establish a CRISPR/Cas9-based strategy for megabase-scale genomic deletions in CHO cells, targeting regions from 3 to over 100 megabases (Mb). Clones carrying deletions of up to 50 Mb were isolated, while a candidate deletion junction spanning 130 Mb was detected in the edited pool, demonstrating the potential for large-scale genome engineering in mammalian cells. Importantly, removal of genomic regions with minimal coding content did not impair growth, viability, or monoclonal antibody productivity. Mechanistic analysis revealed rapid deletion formation and a size-dependent shift in DNA repair pathway usage. Transient inhibition of non-homologous end joining (NHEJ) significantly improved deletion efficiency and clone recovery without compromising cell fitness. These findings establish large-scale genome reduction as a feasible and controllable strategy for rational CHO genome streamlining and the development of next-generation biopharmaceutical cell factories.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":"15 9","pages":"3770–3783"},"PeriodicalIF":4.5,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149003705","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