ACS Synthetic Biology最新文献

Engineered Marine Biofilms for Ocean Environment Monitoring. 用于海洋环境监测的工程海洋生物膜。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-22 DOI: 10.1021/acssynbio.5c00192

Guillermo Nevot, Maria Pol Cros, Lorena Toloza, Nil Campamà-Sanz, Maria Artigues-Lleixà, Laura Aguilera, Marc Güell

{"title":"Engineered Marine Biofilms for Ocean Environment Monitoring.","authors":"Guillermo Nevot, Maria Pol Cros, Lorena Toloza, Nil Campamà-Sanz, Maria Artigues-Lleixà, Laura Aguilera, Marc Güell","doi":"10.1021/acssynbio.5c00192","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00192","url":null,"abstract":"Marine bacteria offer a promising alternative for developing Engineered Living Materials (ELMs) tailored to marine applications. We engineered Dinoroseobacter shibae to increase its surface-associated growth and develop biosensors for ocean environment monitoring. By fusing the endogenous extracellular matrix amyloidogenic protein CsgA with mussel foot proteins, we significantly increased D. shibae biofilm formation. Additionally, D. shibae was engineered to express the tyrosinase enzyme to further enhance microbial attachment through post-translational modifications of tyrosine residues. By exploiting D. shibae's natural genetic resources, two environmental biosensors were created to detect temperature and oxygen. These biosensors were coupled with a CRISPR-based recording system to store transient gene expression in stable DNA arrays, enabling long-term environmental monitoring. These engineered strains highlight D. shibae's potential in advancing marine microbiome engineering for innovative biofilm applications, including the development of natural, self-renewing biological adhesives, environmental sensors, and \"sentinel\" cells equipped with CRISPR-recording technology to capture and store environmental signals.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144367629","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

In-Silico Analysis and Engineering of an Aldehyde/Alcohol Dehydrogenase for Alternative Cofactor Utilization and Selective Butanol Production. 替代辅助因子利用和选择性丁醇生产的醛/醇脱氢酶的硅分析与工程。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-21 DOI: 10.1021/acssynbio.5c00003

Curtis D Moore, Qingke Wang, Geng Wang, Jun Feng, Zhen Qin, Shang-Tian Yang

{"title":"In-Silico Analysis and Engineering of an Aldehyde/Alcohol Dehydrogenase for Alternative Cofactor Utilization and Selective Butanol Production.","authors":"Curtis D Moore, Qingke Wang, Geng Wang, Jun Feng, Zhen Qin, Shang-Tian Yang","doi":"10.1021/acssynbio.5c00003","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00003","url":null,"abstract":"Biobutanol production by solventogenic Clostridia is limited by a low butanol titer and yield. To overcome this limitation, Clostridium tyrobutyricum was engineered to overexpress the adhE2 gene encoding a bifunctional aldehyde/alcohol dehydrogenase (AAD) for converting acetyl-CoA/butyryl-CoA to acetaldehyde/butyraldehyde and then to ethanol/butanol. In this study, we aimed to increase butanol biosynthesis in C. tyrobutyricum by engineering AAD targeting on amino acid residues in the enzyme catalytic center that could increase butanol:ethanol ratios and alter cofactor specificity. In silico mutagenesis and analysis via Rosetta analysis showed that several AAD point mutations could increase butanol production and selectivity over ethanol. We then created C. tyrobutyricum strains overexpressing various AAD mutants. Two AAD mutants, D485G and L488A, engineered to utilize NADPH as the cofactor, increased butanol production by over 100% in batch fermentation, with yields of 0.10-0.13 g/g (vs 0.05 g/g glucose for the wild-type AAD). Two additional AAD mutants, P619G and S601A_V608S_P619G, engineered for increased butanol selectivity, also gave higher butanol yields of 0.13-0.15 g/g. Butanol production further increased to 0.23 g/g when methyl viologen was added to the fermentation. This work leveraged in silico analysis to guide rational engineering of AAD with higher selectivity and activity for butanol production.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144339686","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

Novel FNR-Dependent Oxygen-Responsive Promoters in Escherichia coli: Design, Characterization, and Metabolic Engineering Applications. 大肠杆菌中新型依赖fnr的氧响应启动子：设计、表征和代谢工程应用。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-21 DOI: 10.1021/acssynbio.5c00215

Sen Yang, Wen-Yue Tong, Chao-Hao Guo, Nan Shi, Xiao-Yun Liu, Ming Kang

{"title":"Novel FNR-Dependent Oxygen-Responsive Promoters in Escherichia coli: Design, Characterization, and Metabolic Engineering Applications.","authors":"Sen Yang, Wen-Yue Tong, Chao-Hao Guo, Nan Shi, Xiao-Yun Liu, Ming Kang","doi":"10.1021/acssynbio.5c00215","DOIUrl":"https://doi.org/10.1021/acssynbio.5c00215","url":null,"abstract":"Promoters responsive to changes in cultivation conditions are essential tools for dynamic metabolic engineering. Oxygen-responsive promoters, in particular, exhibit significant application potential in oxygen-limited fermentation processes. However, currently reported oxygen-dependent promoters exhibit limited dynamic ranges, and notably, there remains a lack of research on oxygen-responsive negatively regulated promoters. In this study, we designed and characterized a series of dissolved oxygen-responsive promoters in Escherichia coli under the regulation of the transcription factor fumarate-nitrate reduction (FNR). Anaerobically activated promoters were constructed by inserting FNR binding site (FBS) upstream of inducible core promoters, while anaerobically repressed promoters were developed by inserting FBS downstream of or flanking constitutive promoters. The most effective anaerobically activated promoters showed 24-138-fold higher activity under anaerobic conditions compared to aerobic conditions. Under anaerobic conditions, promoters with DNA looping-mediated anaerobic repression maintained only 8-17% of the activity observed under aerobic conditions. These promoters were specifically regulated by FNR, as confirmed by tests in a DH5α Δfnr strain, and responded rapidly to oxygen depletion (within 30 min). The utility of these genetic tools was demonstrated by applying them to enhance pyruvate production in E. coli. An engineered strain with anaerobic-repressed aceE and anaerobic-activated atpAGD genes produced 5.76 g/L pyruvate at 55.7% yield in shake flask fermentations. This study offers an expanded toolbox of oxygen-responsive promoters that enable precise gene regulation based on dissolved oxygen levels, providing novel genetic strategies for developing efficient two-stage fermentation processes with separated growth and production phases.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144339687","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

Sensitive and Broadly Compatible Transcription Factor-Based Biosensor for Monitoring c-di-GMP Dynamics in Biofilms. 灵敏和广泛兼容的基于转录因子的生物传感器监测生物膜中的c-二gmp动力学。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-16 DOI: 10.1021/acssynbio.5c00193

Yidan Hu, Jian Liu, Aloysius Teng, Yingdan Zhang, Liang Yang, Bin Cao

{"title":"Sensitive and Broadly Compatible Transcription Factor-Based Biosensor for Monitoring c-di-GMP Dynamics in Biofilms.","authors":"Yidan Hu, Jian Liu, Aloysius Teng, Yingdan Zhang, Liang Yang, Bin Cao","doi":"10.1021/acssynbio.5c00193","DOIUrl":"10.1021/acssynbio.5c00193","url":null,"abstract":"Biofilms are ubiquitous and have many negative effects, for example, in infections or biocorrosion. Given the critical role of the second messenger cyclic di-GMP (c-di-GMP) in biofilm formation, targeting a reduction in intracellular concentrations of c-di-GMP is believed to be a key aspect in the development of biofilm mitigation strategies. To facilitate this effort, here, we developed a transcription factor (TF)-based biosensor that integrates the TF FleQ from Pseudomonas aeruginosa with a PR-Ppel tandem promoter. The dynamic range of the biosensor was optimized by fine-tuning the TF expression. The biosensor exhibited broad compatibility and effectiveness in detecting decreases in c-di-GMP levels across various biofilm model organisms, including strains lacking FleQ or its homologues, such as Escherichia coli, Shewanella oneidensis, Comamonas testosteroni, and Acinetobacter baumannii, as well as P. aeruginosa containing FleQ. Additionally, we monitored c-di-GMP levels in biofilms formed by P. aeruginosa and S. oneidensis through a ratiometric, image-based quantification method. The methodology used the green fluorescence protein (GFP) as a reporter for c-di-GMP levels and 4',6-diamidino-2-phenylindole (DAPI) or the monomeric red fluorescence protein (mRFP) as the indicator for biofilm biomass. The GFP/DAPI or GFP/mRFP ratio gives effective c-di-GMP per unit of biomass. This TF-based biosensor provides an important tool to study c-di-GMP dynamics, which facilitates efforts in developing biofilm control strategies and understanding regulatory networks for biofilm development.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2316-2327"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074898","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

Bacterial Cells Engineered with Synthetic Genetic Materials for Blind Testing of Random Mutagenesis. 用合成遗传材料工程化细菌细胞进行随机诱变盲试验。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-12 DOI: 10.1021/acssynbio.5c00054

Qian Liu, Zhaoguan Wang, Jingsong Cui, Jiawei Li, Changyue Jiang, Gaoxu Tan, Hao Qi

{"title":"Bacterial Cells Engineered with Synthetic Genetic Materials for Blind Testing of Random Mutagenesis.","authors":"Qian Liu, Zhaoguan Wang, Jingsong Cui, Jiawei Li, Changyue Jiang, Gaoxu Tan, Hao Qi","doi":"10.1021/acssynbio.5c00054","DOIUrl":"10.1021/acssynbio.5c00054","url":null,"abstract":"Synthetic genetic materials, particularly those in genetically modified organisms (GMOs) deployed into complex environments, necessitate robust postmarket surveillance for continuous monitoring of both the materials and their applications throughout their lifecycle. Here, we introduce novel-coded genomic material for a blind mutation test that evaluates mutagenesis in synthetic genomic sequences without requiring direct sequence comparison. This test utilizes a Genome-Digest, which is embedded within essential genes, establishing mathematical correlation between the nucleotide sequence and codon order. This novel design allows for independent assessment of mutations by decoding the nucleotide sequence, thereby eliminating the need for reference sequences or extensive bioinformatic analysis. Furthermore, the test has the capability to analyze mixed genomic materials from a single sample and can be extended to the pooled testing of multiple samples as well. Building on this framework, we propose the 'Genome-ShockWatch' methodology. In proof-of-concept trials, it successfully detected mutations that exceeded a predefined threshold in long-read sequencing data from a yogurt sample containing Genome-Digest encoded Nissle 1917 E. coli cells and naturally occurring probiotic bacteria. Consequently, the Genome-Digest system provides a robust foundation for the routine surveillance and management of GMOs and related synthetic products, ensuring their safety and efficacy in diverse environmental contexts.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2139-2150"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951119","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

Translational Enhancer Based Amplification of Toehold Sensors (TacToe) for Improved Sensitivity and Speed of Viral RNA Detection. 基于翻译增强子的脚传感器（TacToe）扩增提高病毒RNA检测的灵敏度和速度。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-29 DOI: 10.1021/acssynbio.4c00861

Tanvi Kale, Rudvi Pednekar, Séverine Marianne Cazaux, Valentina Ferrando Letelier, Justin R J Vigar, Fernán Federici, Keith Pardee, Chaitanya A Athale

{"title":"Translational Enhancer Based Amplification of Toehold Sensors (TacToe) for Improved Sensitivity and Speed of Viral RNA Detection.","authors":"Tanvi Kale, Rudvi Pednekar, Séverine Marianne Cazaux, Valentina Ferrando Letelier, Justin R J Vigar, Fernán Federici, Keith Pardee, Chaitanya A Athale","doi":"10.1021/acssynbio.4c00861","DOIUrl":"10.1021/acssynbio.4c00861","url":null,"abstract":"Toehold switches are RNA riboswitches activated by complementary nucleic acid sequences that have shown promise as point-of-care (PoC) molecular diagnostics. However, typical implementations require an additional nucleic-acid-sequence-specific amplification step. Here, we describe a novel toehold switch with a T7-g10 translational enhancer (Tac) that amplifies the expression of the reporter gene regulated by toehold (Toe) sensors. We compare such a TacToe sensor to a previously developed sensor for detecting short RNA sequences from the Zika virus (ZIKV). We demonstrate that this one-step TacToe sensor in a transcription-translation (TxTl) reaction has an improved sensitivity to RNA and a faster time of detection, compared to the conventional toehold. Replacing the ZIVK sequence with a segment of the N-gene of SARS-nCoV, we demonstrate up to a picomolar sensitivity. Qualitatively comparable results are observed in Escherichia coli cell lysate-based homemade cell free extract (CFE), demonstrating the robustness and utility of these sensors in low-resource settings.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"1920-1930"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172088","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

Gene Expression Depends on the Interplay Among Growth, Resource Biogenesis, and Nutrient Quality. 基因表达取决于生长、资源生物发生和营养品质之间的相互作用。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-29 DOI: 10.1021/acssynbio.4c00828

Juhyun Kim, Alexander P S Darlington, Said Muñoz-Montero, Rafael Montenegro, Perrine Dalby, Noemí Herrera-Martín, Alice Banks, Satya Prakash, Karen Polizzi, Declan G Bates, José I Jiménez

{"title":"Gene Expression Depends on the Interplay Among Growth, Resource Biogenesis, and Nutrient Quality.","authors":"Juhyun Kim, Alexander P S Darlington, Said Muñoz-Montero, Rafael Montenegro, Perrine Dalby, Noemí Herrera-Martín, Alice Banks, Satya Prakash, Karen Polizzi, Declan G Bates, José I Jiménez","doi":"10.1021/acssynbio.4c00828","DOIUrl":"10.1021/acssynbio.4c00828","url":null,"abstract":"The gene expression capacity of bacteria depends on the interplay between growth and the availability of the transcriptional and translational machinery. Growth rate is accepted as the physiological parameter controlling the allocation of cellular resources. Understanding the relationship between growth and resources is key for the efficient design of genetic constructs, but it is obscured by the mutual dependence between growth and gene expression. In this work, we investigate the contributions of molecular factors, growth rate, and metabolism to gene expression by investigating the behavior of bacterial cells grown in chemostats. Using a model of the whole cell and validating it experimentally, our results show that while growth rate and molecular factors, such as the number of rRNA operons, set the abundance of transcriptional and translational machinery, it is metabolism that governs the usage of resources by tuning elongation rates. We show, using a biotechnologically relevant example, that gene expression capacity can be maximized using low growth in a high-quality medium. These findings unveil fundamental trade-offs in physiology that will inform future bioprocess optimization.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2012-2029"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179541","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

Enhanced Thermal Stability of NADH/NAD⁺ through Tethering to Silica Nanoparticles. 纳米二氧化硅系缚增强NADH/NAD+的热稳定性。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-06-04 DOI: 10.1021/acssynbio.5c00348

Rowan McDonough, Charlotte C Williams, Carol J Hartley, Nigel G French, Colin Scott, David A Lewis

{"title":"Enhanced Thermal Stability of NADH/NAD+ through Tethering to Silica Nanoparticles.","authors":"Rowan McDonough, Charlotte C Williams, Carol J Hartley, Nigel G French, Colin Scott, David A Lewis","doi":"10.1021/acssynbio.5c00348","DOIUrl":"10.1021/acssynbio.5c00348","url":null,"abstract":"The poor thermal stability of the cofactor β-nicotinamide adenine dinucleotide (NAD+) in industrial settings can be a limiting factor in the expansion of biosynthetic approaches to chemical production. In this work, we report that the half-life of SiNP-tethered NAD+ when stored in solution at 37 °C, and subsequently catalyzed by glycerol-3-phosphate dehydrogenase from E. coli (EcG3PD) at ambient temperature, is increased 11-fold to over 500 h, compared with 34.5 h for free NAD+. Similarly, the half-life for the degradation of the tethered NAD+ stored at 100 °C was 5 h compared with 0.3 h for free NAD+ corresponding to a 15-fold enhancement in the retention of activity of tethered NAD+. Kinetic analysis indicates that activity loss of NAD+ is similar to that of the normal hydrolysis mechanism, with the difference likely being due to steric effects and access to labile bonds. We also demonstrated that the retention of reactivity of heat-treated EcG3PD adsorbed to the surface NAD+-functionalized particles was improved compared to freely diffusing EcG3PD and NAD+ at ambient temperature, consistent with our previous work which showed a surface-localized enzyme/substrate interaction resulting in a concentrating effect. These results demonstrate the great potential for the long-term use of tethered NAD+ and enzymes, even at high operational temperatures, in biocatalytic applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2368-2374"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223704","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

Standardized Quorum Sensing Tools for Gram-Negative Bacteria. 革兰氏阴性菌标准化群体感应工具。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-06-06 DOI: 10.1021/acssynbio.5c00036

Paula Múgica-Galán, Jesús Miró-Bueno, Ángeles Hueso-Gil, Pablo Japón, Ángel Goñi-Moreno

引用次数: 0

The Japan-UK Synthetic Biology Conference, Spring 2025: Strengthening Global Links to Engineer Biology 日本-英国合成生物学会议，春季2025：加强与工程生物学的全球联系

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 DOI: 10.1021/acssynbio.5c0023210.1021/acssynbio.5c00232

Thomas E. Gorochowski*, Michael A. Brockhurst, Francesca Ceroni, Yuka W. Iwasaki and Nozomu Yachie,

引用次数: 0