{"title":"Trusted Codon Fingerprint: A Streamlined Platform for Deep and Reversible Bacterial Cell Labeling.","authors":"Zhaoguan Wang, Jingsong Cui, Gaoxu Tan, Gaili Cao, Jie Zhang, Hao Qi","doi":"10.1021/acssynbio.5c00263","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00263","url":null,"abstract":"<p><p>The proliferation of artificially engineered cells, driven by advances in synthetic biology, underscores the urgent need to efficiently and precisely tag or identify these synthetic entities, ensuring robust management, oversight, and traceability. Here, we present a platform called trusted codon fingerprint (TCF), which leverages synonymous codon substitutions to integrate identification information into the open reading frames of antibiotic-resistant genes on a plasmid, thereby establishing unique codon fingerprints for target cells. TCF is devised for streamlined and erasable cell labeling with favorable identification capabilities. The dual mechanisms consist of antibiotic selection, which eliminates nearly all incorrectly assembled antibiotic-resistant genes, and error-correcting codes, which accommodate the rest of the minor substitutions. These features eliminate the necessity for a validation step and significantly streamline the process of writing TCF into cells, with cell viability guaranteeing the label's proper functioning. Through evaluating thousands of clones, TCF has achieved 100% writing efficiency and successful identification of the host cell genome via hash function computation using long-read sequencing. Finally, by using a temperature-sensitive plasmid backbone, an <i>Escherichia coli</i> strain engineered through 10-step genome modifications was recorded by TCF in a time- and labor-efficient manner, enabling cyclic writing and erasure of cell labels. Consequently, the TCF labeling system provides a streamlined, erasable, and effective tool, facilitating regulatory compliance and enhancing the flexibility for identity management of engineered strains.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145123847","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}
{"title":"Neural CRNs: A Natural Implementation of Learning in Chemical Reaction Networks.","authors":"Rajiv Teja Nagipogu, John H Reif","doi":"10.1021/acssynbio.5c00099","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00099","url":null,"abstract":"<p><p>Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have primarily relied on emulating discrete-layered neural architectures using steady-state computations of mass action kinetics. Here, we propose an alternative approach where the neural computations are modeled using the continuous-time evolution of molecular concentrations. The analog nature of our framework naturally aligns with chemical kinetics-based computation, resulting in practically viable circuits. We present the advantages of our framework through three key demonstrations: (1) we assemble an end-to-end supervised learning pipeline using only two sequential phases, the minimum required number for supervised learning; (2) we show (through appropriate simplifications) that both linear and nonlinear modeling circuits can be implemented solely using unimolecular and bimolecular reactions, avoiding the complexities of higher-order chemistries; and (3) we show how first-order gradient approximations can be natively incorporated into the framework, enabling nonlinear models to scale linearly rather than combinatorially with input dimensionality. All the circuit constructions are validated through training and inference simulations across various regression and classification tasks. Our work presents a viable pathway toward embedding learning behaviors in synthetic biochemical systems.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111584","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}
{"title":"HinZip: Combining Hin Recombinase and FosW to Mimic HD-Zip Plant Proteins.","authors":"Raneem Akel, Rama Edaibis, Jumi A Shin","doi":"10.1021/acssynbio.5c00386","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00386","url":null,"abstract":"<p><p>Small customized proteins that bind specific DNA sequences in a genome could serve as powerful tools for synthetic biology and therapeutic applications. These proteins could regulate gene circuits or act as precision-targeted inhibitors in disease networks. Here, we designed HinZip, a protein engineered to bind a unique 24+ base-pair DNA sequence with high affinity and specificity, thereby minimizing off-target effects. HinZip is inspired by the HD-Zip (homeodomain-leucine zipper) transcription factor family, which exists only in plants. <i>No high-resolution structures exist for HD-Zip</i>: genome-wide analyses indicate that HD-Zips use a homeodomain to bind DNA and a leucine zipper for dimerization. To emulate this functionality, we fused the Hin recombinase DNA-binding domain with the FosW leucine zipper. Electrophoretic mobility shift assays confirmed HinZip's cooperative binding to a 29 base-pair inverted <i>HixC</i> palindrome (<i>K</i><sub>d</sub> = 17 nM), with no detectable binding to nonspecific DNA at protein concentrations up to 2 μM. Circular dichroism and dynamic light scattering further support dimer formation. Additionally, the bacterial one-hybrid assay demonstrated HinZip's sequence-specific binding in cellulo. Even in the absence of structural guidance, we successfully designed a functional \"frankenprotein\" by integrating unrelated protein modules. This work underscores the feasibility of engineering bespoke DNA-binding proteins for targeted genomic interactions.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111528","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}
Kun Liu, Xinlan Fan, Ming Zhao, Yu Chen, Qinghui Tang, Shenghua Wei, Zhenglian Xue, Dongzhi Wei, Feng-Qing Wang
{"title":"Structure-Guided Design of Artificial Transcription Factor for a Progesterone Biosensor.","authors":"Kun Liu, Xinlan Fan, Ming Zhao, Yu Chen, Qinghui Tang, Shenghua Wei, Zhenglian Xue, Dongzhi Wei, Feng-Qing Wang","doi":"10.1021/acssynbio.5c00488","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00488","url":null,"abstract":"<p><p>Transcription factors (TFs) can be used in genetic circuits and biosensors in the field of synthetic biology. Traditionally, TFs derived from prokaryotic organisms are transferred to more complex eukaryotic cells to achieve gene control; however, TFs in eukaryotes are rarely transferred to prokaryotes. Herein, an artificial TF responsive to progesterone was designed through MD simulations, and the linker fine-tuned the convergence of the DNA-binding domain and activation domain as the desired conformation guide to design an artificial TF ProB assembled from the QF<sub>DBD</sub>, the ligand-binding domain, linker, and QF<sub>AD</sub>. The ProB acted on the synthetic promoter QT, which is composed of QUAS, 10-bp space, T7, and the RBS, which controlled the transcription of the biosensor GFP in <i>E. coli</i>. The performance of the whole-cell progesterone biosensor was optimized via a bacterial enrichment strategy, which made the biosensor highly sensitive (LOD 0.15 μg/L and EC<sub>50</sub> 26.58 μg/L), preferably in the working temperature range (20-30 °C), with only a 56.4 min detection time and a working concentration range of 0.15-40 μg/L, and the performance reached the requirements of clinical application. This report presents effective strategies and valuable insights into the design of non-natural TFs and their artificial systems in prokaryotes.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111547","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}
{"title":"Metabolic Engineering of Microbial Chassis Cells for d-Pantothenate Production: A Review.","authors":"Fang-Ying Zhu, Yun-Yue Gu, Xue Cai, Jun-Ping Zhou, Yuan-Yuan Chen, Yi-Hong Wang, Bo Zhang, Zhi-Qiang Liu, Yu-Guo Zheng","doi":"10.1021/acssynbio.5c00283","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00283","url":null,"abstract":"<p><p>d-Pantothenate (DPA), an essential functional compound, has experienced increasing market demand due to its widespread applications across the pharmaceutical, cosmetic, and animal feed industries. While numerous microbial classic strains have been engineered for DPA synthesis via microbial fermentation as an alternative to conventional chemoenzymatic synthesis, a comprehensive analysis of the metabolic engineering strategies employed for these microbial chassis cells for DPA production remains absent. This review systematically delineates the DPA metabolic pathway, encompassing β-alanine and pantoate metabolic modules, the regulatory network, and transport systems, and highlights the main regulatory mechanisms of operons and genes involved in the DPA biosynthesis pathway. The current research status in metabolic engineering strategies for manipulating DPA-producing strains is summarized and analyzed to elucidate the current trends and insights for further engineering. Finally, current challenges and future perspectives for the sustainable production of DPA are discussed, and guidelines for reducing production costs are proposed.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111474","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}
Sebastian Barthel, Maximilian Hoffmann-Becking, Islomjon G Karimov, Tobias J Erb
{"title":"Genetically Encoded Control of <i>In Vitro</i> Transcription-Translation Coupled DNA Replication.","authors":"Sebastian Barthel, Maximilian Hoffmann-Becking, Islomjon G Karimov, Tobias J Erb","doi":"10.1021/acssynbio.5c00477","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00477","url":null,"abstract":"<p><p>The bottom-up reconstruction of cellular functions has gained increasing attention for studying biological complexity and for developing advanced biotechnological tools, including synthetic cells. A fundamental challenge is the ability to control and replicate DNA-encoded information within basic <i>in vitro</i> transcription-translation (IVTT) systems. Here, we constructed a transcription-translation coupled DNA replication (TTcDR) system that is based on a modified PURE (<u>P</u>rotein synthesis <u>U</u>sing <u>R</u>ecombinant <u>E</u>lements) IVTT system and Φ29 DNA polymerase, which is controlled by external signals. To this end, we first established and characterized a PUREfrex 1.0-based TTcDR system. We then constructed and optimized TetR-based control of TTcDR activity, either by DNA-encoded TetR or by supplying purified TetR. Our final DNA-encoded TetR circuit allows ∼1000-fold DNA replication, ∼100-fold repression, and ∼4-fold induction with anhydrotetracycline. Our results demonstrate the potential and challenges of controlling <i>in vitro</i> DNA replication, for example, for the evolution of <i>in vitro</i> systems.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084520","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}
Jikai Zong, Kaixing Xiao, Dan Wang, Yaqi Kang, Zhiyao Peng, Bo Yu
{"title":"Retraction of \"Novel Reprogramming of Polyketide Synthase for Valerolactam Production\".","authors":"Jikai Zong, Kaixing Xiao, Dan Wang, Yaqi Kang, Zhiyao Peng, Bo Yu","doi":"10.1021/acssynbio.5c00619","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00619","url":null,"abstract":"","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084552","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}
Dennis Tin Chat Chan, Johan Bjerg, Hans C Bernstein
{"title":"Broad-Host-Range Synthetic Biology: Rethinking Microbial Chassis as a Design Variable.","authors":"Dennis Tin Chat Chan, Johan Bjerg, Hans C Bernstein","doi":"10.1021/acssynbio.5c00308","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00308","url":null,"abstract":"<p><p>Broad-host-range synthetic microbiology is redefining the role of microbial hosts in genetic design by moving beyond the traditional organisms. Historically, synthetic biology has focused on optimizing engineered genetic constructs within a limited set of well-characterized chassis, often treating host-context dependency as an obstacle. However, emerging research demonstrates that host selection is a crucial design parameter that influences the behavior of engineered genetic devices through resource allocation, metabolic interactions, and regulatory crosstalk. By leveraging microbial diversity, broad-host-range synthetic biology enhances the functional versatility of engineered biological systems, enabling a larger design space for biotechnology applications in biomanufacturing, environmental remediation, and therapeutics. The continued development of broad-host-range tools─including modular vectors and host-agnostic genetic devices─facilitates the expansion of chassis selection, improving system predictability and stability. This perspective highlights the advantages of incorporating host selection into synthetic biology design principles, positioning microbial chassis as tunable components rather than passive platforms.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079090","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}
Yan-Fang Nie, Sheng-Jie Yue, Peng Huang, Ding-Kang Hu, Zheng Xu, Alejandro Aguilar-Vera, José Utrilla Carreri, Xue-Hong Zhang, Hong-Bo Hu
{"title":"Harnessing the Endogenous Type I-F CRISPR/Cas System for Efficient Genome Engineering and Gene Repression in <i>Pseudomonas chlororaphis</i> LX24.","authors":"Yan-Fang Nie, Sheng-Jie Yue, Peng Huang, Ding-Kang Hu, Zheng Xu, Alejandro Aguilar-Vera, José Utrilla Carreri, Xue-Hong Zhang, Hong-Bo Hu","doi":"10.1021/acssynbio.5c00371","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00371","url":null,"abstract":"<p><p><i>Pseudomonas chlororaphis</i>, a nonpathogenic plant growth-promoting rhizobacterium, holds immense potential for agricultural and industrial applications due to its ability to biosynthesize bioactive metabolites. However, the lack of efficient genetic tools has hindered its metabolic engineering. In this study, we first characterized an endogenous type I-F CRISPR/Cas system in <i>P. chlororaphis</i> LX24 and established a programmable genome editing toolkit based on this system. Concurrently, the plasmid transformation efficiency of <i>P. chlororaphis</i> LX24 was enhanced by identifying and deleting the restriction-modification systems. We further demonstrated the DNA interference capability with different PAM sequences of the type I-F CRISPR/Cas system, which also exhibited various editing efficiencies ranging from 22 to 87% in <i>P. chlororaphis</i> LX24. By introducing the λ-Red recombination system, the knockout efficiency of the phenazine cluster (8.3 kb) increased by over 9-fold. Next, introducing the <i>sacB</i>-based counterselection marker achieved a 100% plasmid curing success within 36 h. The optimized toolkit was further applied to single-step gene insertion and replacement with 100% success rates. Additionally, we established a CRISPR interference (CRISPRi) system for transcriptional repression in <i>P. chlororaphis</i> LX24 by knocking out nuclease Cas3. Through modulating the induction time and concentration of IPTG, the production of phenazines was reduced to 21-89% within 24 h in <i>P. chlororaphis</i> LX24. Overall, our work developed a convenient and precise genetic tool for the <i>P. chlororaphis</i> LX24, and the methods may also provide a reference for repurposing endogenous CRISPR systems in non-model prokaryotes.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079106","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}
{"title":"Development of a High Anthraquinone-Producing <i>Escherichia coli</i> Strain Using Malonyl-CoA Supply Pathway Engineering.","authors":"Takatoshi Suematsu, Manami Takama, Itsuki Tomita, Shumpei Asamizu, Takahiro Bamba, Tomohisa Hasunuma","doi":"10.1021/acssynbio.5c00354","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00354","url":null,"abstract":"<p><p>Anthraquinones are valuable compounds that are traditionally used as natural pigments and have diverse pharmacological activities, including antimicrobial and anticancer effects. In this study, we aimed to enhance the production of 1,3,5-trihydroxyanthraquinone (AQ256) using <i>Escherichia coli</i> (<i>E. coli</i>) as a host. AQ256 is biosynthesized from eight malonyl-CoA molecules via the type II polyketide synthase pathway. However, previous studies have reported very low production levels of AQ256 in <i>E. coli</i> (approximately 2.5 mg/L), mainly because of limited malonyl-CoA availability. To address this, we introduced a heterologous malonate assimilation pathway and reinforced the endogenous malonyl-CoA biosynthesis pathway. An <i>E. coli</i> strain harboring AQ256 biosynthetic genes from <i>Photorhabdus laumondii</i> TTO1 produced only 1.3 mg/L AQ256. Upon introducing the malonate assimilation pathway and cultivating in malonate-supplemented Luria-Bertani medium, production increased to 3.8 mg/L. Further enhancement of the endogenous malonyl-CoA supply through the coexpression of pantothenate kinase and acetyl-CoA carboxylase resulted in strain AQ-04, which produced 12.3 mg/L AQ256. Optimization of cultivation conditions enabled AQ-04 to achieve 23.9 mg/L AQ256, a 9.6-fold increase compared to previous studies. Our results demonstrate that the combination of introducing a malonate assimilation pathway and enhancing native malonyl-CoA supply is a highly effective strategy for increasing malonyl-CoA availability. This approach is promising for the biosynthesis of a wide range of malonyl-CoA-derived compounds.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074040","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}