ACS Synthetic Biology最新文献_第2页

Systematic Engineering for Efficient Uric Acid-Degrading Activity in Probiotic Yeast Saccharomyces boulardii. 博氏酵母菌尿酸高效降解活性的系统工程研究。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-08 DOI: 10.1021/acssynbio.4c00831

Wenzhuo Wang, Lei Pan, Huansha He, Huiyuan Xue, He Huang, Audrey Mihewi Samosir, Xian Fu, Yue Shen

{"title":"Systematic Engineering for Efficient Uric Acid-Degrading Activity in Probiotic Yeast Saccharomyces boulardii.","authors":"Wenzhuo Wang, Lei Pan, Huansha He, Huiyuan Xue, He Huang, Audrey Mihewi Samosir, Xian Fu, Yue Shen","doi":"10.1021/acssynbio.4c00831","DOIUrl":"10.1021/acssynbio.4c00831","url":null,"abstract":"Hyperuricemia, caused by uric acid disequilibrium, is a prevalent metabolic disease that most commonly manifests as gout and is closely associated with a spectrum of other comorbidities such as renal disorders and cardiovascular diseases. While natural and engineered probiotics that promote catabolism of uric acid in the intestine have shown promise in relieving hyperuricemia, limitations in strain efficiency and the requirements for achieving high performance remain major hurdles in the practical application of probiotic-mediated prevention and management. Here, we employed a systematic strategy to engineer a high-efficiency uric acid catabolism pathway in S. cerevisiae. An uricase from Vibrio vulnificus, exhibiting high-level activity in S. cerevisiae, was identified as the uric acid-degrading component. The expression level and stability of urate transporter UapA were improved by constructing a chimera, enabling reliable uric acid import in S. cerevisiae. Additionally, constitutive promoters were selected and combinatorially assembled with the two functional components, creating a collection of pathways that confer varied levels of uric acid catabolic activity to S. cerevisiae. The best-performing pathway can express uric acid-degrading activity up to 365.32 ± 20.54 μmol/h/OD, requiring only simple cultivation steps. Eventually, we took advantage of the genetic similarity between model organism S. cerevisiae and probiotic S. boulardii and integrated the optimized pathway into identified high-expression integration loci in the S. boulardii genome. The activity can be stably maintained under high-density fermentation conditions. Overall, this study provided a high-potential hyperuricemia-managing yeast probiotic strain, demonstrating the capabilities of developing recombinant probiotics.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2030-2043"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952068","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

Rewiring Estrogen Receptor α into Bisphenol Selective Receptors Using Darwin Assembly-Based Directed Evolution (DADE) in Saccharomyces cerevisiae. 利用达尔文组装定向进化（DADE）在酿酒酵母中将雌激素受体α重新连接为双酚选择性受体。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-10 DOI: 10.1021/acssynbio.5c00163

Roy Eerlings, Xiao Yin Lee, Wout Van Eynde, Lisa Moris, Sarah El Kharraz, Elien Smeets, Wout Devlies, Frank Claessens, Kevin J Verstrepen, Arnout Voet, Christine Helsen

{"title":"Rewiring Estrogen Receptor α into Bisphenol Selective Receptors Using Darwin Assembly-Based Directed Evolution (DADE) in Saccharomyces cerevisiae.","authors":"Roy Eerlings, Xiao Yin Lee, Wout Van Eynde, Lisa Moris, Sarah El Kharraz, Elien Smeets, Wout Devlies, Frank Claessens, Kevin J Verstrepen, Arnout Voet, Christine Helsen","doi":"10.1021/acssynbio.5c00163","DOIUrl":"10.1021/acssynbio.5c00163","url":null,"abstract":"Bisphenols are widely used in manufacturing plastics and resins, but their environmental persistence raises concerns to human health and ecosystems. Accurate measurements for bisphenols are crucial for effective monitoring and regulation. Analytical methods detect only preselected bisphenols, while bioassays assessing estrogen receptor α activation suffer from poor sensitivity and strong background signals due to estrogenic contaminations. To develop a bioassay in Saccharomyces cerevisiae with increased sensitivity and specificity for bisphenols, we performed multi-site directed mutagenesis and directed evolution of more than 108 stably integrated estrogen receptor variants. By mutating the estrogen receptor α towards recognition of bisphenol A in yeast, we determined the preBASE variant (M421G_V422G_V533D_L536G_Y537S) with elevated bisphenol A sensitivity (EC50:329 nM) and lost estrogen responsiveness (EC50:0,17 mM). Further engineering yielded an off-target mutant, identified as the Bisphenol-Affinity and Specificity-Enhanced (BASE) variant (M421G_V422G_V533D_L536G_Y537S_L544I) that uses bisphenols as its primary agonist (EC50:32 mM) and impaired estrogen sensitivity (EC50:85M). The rewiring into a bisphenol receptor was confirmed in ligand binding assays to purified ligand binding domains. Taken together, the identified variants form stepping stones for further protein engineering to generate bisphenol specific high-throughput yeast-based bioassays.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2254-2269"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956139","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

Genetic Toggle Switch in Plants. 植物的基因开关。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-19 DOI: 10.1021/acssynbio.4c00777

Tessema K Kassaw, Wenlong Xu, Christopher S Zalewski, Katherine Kiwimagi, Ron Weiss, Mauricio S Antunes, Ashok Prasad, June I Medford

{"title":"Genetic Toggle Switch in Plants.","authors":"Tessema K Kassaw, Wenlong Xu, Christopher S Zalewski, Katherine Kiwimagi, Ron Weiss, Mauricio S Antunes, Ashok Prasad, June I Medford","doi":"10.1021/acssynbio.4c00777","DOIUrl":"10.1021/acssynbio.4c00777","url":null,"abstract":"In synthetic biology, genetic components are assembled to make transcriptional units, and transcriptional units are assembled into circuits to perform specific and predictable functions of a genetic device. Genetic devices have been described in bacteria, mammalian cell cultures, and small organoids, yet the development of programmable genetic circuits for devices in plants has lagged. Programmable genetic devices require defining the component's quantitative functions. Because plants have long life spans, studies often use transient analysis to define quantitative functions, while verification in stably engineered plants is often neglected and largely unknown. This raises the question if unique attributes of plants, such as environmental sensitivity, developmental plasticity, or alternation of generations, adversely impact predictability of plant genetic circuits and devices. Alternatively, it is also possible that genetic elements to produce predictable genetic devices for plants require rigorous characterization with detailed mathematical modeling. Here, we use plant genetic elements with quantitatively characterized transfer functions and developed in silico models to guide their assembly into a genetic device: a toggle switch or a mutually inhibitory gene-regulatory device. Our approach allows for computational selection of plant genetic components and iterative refinement of the circuit if the desired genetic functions are not initially achieved. We show that our computationally selected genetic circuit functions as predicted in stably engineered plants, including through tissue and organ differentiation. Developing abilities to produce predictable and programmable plant genetic devices opens the prospect of predictably engineering plant's unique abilities in sustainable human and environmental systems.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"1988-2001"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092001","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 Encapsidated TRV1 as a Complete VIGS Platform. 工程封装TRV1作为一个完整的VIGS平台。

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.5c00153

Alexander C Pfotenhauer, Samantha M Jones, Mikayla Clark, Bryn L Concha, Elliot B Goldstein, Stacee Harbison, Lana H Martin, D Nikki Reuter, Andrew C Reed, C Neal Stewart, Scott C Lenaghan

{"title":"Engineering Encapsidated TRV1 as a Complete VIGS Platform.","authors":"Alexander C Pfotenhauer, Samantha M Jones, Mikayla Clark, Bryn L Concha, Elliot B Goldstein, Stacee Harbison, Lana H Martin, D Nikki Reuter, Andrew C Reed, C Neal Stewart, Scott C Lenaghan","doi":"10.1021/acssynbio.5c00153","DOIUrl":"10.1021/acssynbio.5c00153","url":null,"abstract":"Tobacco rattle virus (TRV) is a bipartite single-stranded RNA virus that encodes a replicase, movement protein, and silencing suppressor on TRV1 and a capsid protein on TRV2. Researchers typically insert target silencing sequences into TRV2 and coexpress this with TRV1 to achieve virus-induced gene silencing (VIGS). However, TRV1 does not require TRV2 for mobility or replication within a plant host. With this knowledge, we engineer TRV1 alone as a self-replicating RNA (srRNA) that moves systemically throughout plants for targeted gene repression of up to 89%. As TRV1 is encapsidated in trans by the capsid protein encoded on TRV2, we demonstrate the ability to encapsidate our TRV1 srRNAs for application to target plants by coexpression of the capsid protein off a nonviral expression vector. The subsequent encapsidated TRV1 srRNA can then be harvested and applied to new plants by using a simple spray-on application. Since the RNA for the capsid does not accompany the TRV1 srRNA, our srRNAs are incapable of spreading from plant to plant after the initial application. Minimal to no phenotypic penalties were observed when we used our spray-on srRNA approach. To our knowledge, this is the first demonstration of engineering a sprayable TRV1-based srRNA that is highly capable of repressing target genes. As TRV has a broad host range and our encapsidated srRNAs are unlikely to persist in the environment, we envision that this platform can be used for targeted gene silencing in agriculture.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2230-2240"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172080","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

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.5c00232

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

引用次数: 0

Optimized Phage Display-Based Selection for the Development of Heterodimerizing Optogenetic Tools. 基于噬菌体展示的优化选择开发异二聚化光遗传工具。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-08 DOI: 10.1021/acssynbio.5c00167

Giang N T Le, Jaewan Jang, Maruti Uppalapati, G Andrew Woolley

引用次数: 0

De Novo Synthesis of Tyrosol and Hydroxytyrosol through Temperature-Inducible Systems and Metabolic Engineering. 利用温度诱导系统和代谢工程从头合成酪醇和羟基酪醇。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-23 DOI: 10.1021/acssynbio.5c00172

Xiaochuan Chen, Tao Qian, Wenping Wei, Yihui Zhu, Gaopan Cai, Mengfan Li, Xiaohe Chu, Bang-Ce Ye

{"title":"De Novo Synthesis of Tyrosol and Hydroxytyrosol through Temperature-Inducible Systems and Metabolic Engineering.","authors":"Xiaochuan Chen, Tao Qian, Wenping Wei, Yihui Zhu, Gaopan Cai, Mengfan Li, Xiaohe Chu, Bang-Ce Ye","doi":"10.1021/acssynbio.5c00172","DOIUrl":"10.1021/acssynbio.5c00172","url":null,"abstract":"Hydroxytyrosol (HT) has various biological and pharmacological activities, including potent antioxidant activity. The efficient synthesis of HT and tyrosol has been achieved by microbial synthesis. However, more strategies are needed to enhance its yield and meet the demands of industrialization. In this study, SceARO10 and EcoyahK were used for the de novo synthesis of tyrosol in Escherichia coli using a temperature-inducible system. Different sources of phenolic acid decarboxylase and alcohol reductase were investigated, with YliARO10 and YliPAR4 from Yarrowia lipolytica showing the best catalytic performance, yielding 4.05 g/L of tyrosol at 60 h in shake flasks, the highest yield reported. Next, EblHpaBC from E. coli BL21 (DE3) was introduced for HT biosynthesis, and the HT-related degradation gene mhpB was functionally characterized in E. coli. Subsequently, by enhancing precursor supply, eliminating competing metabolic pathways, and knocking out mhpB, the HT yield reached 1.28 g/L after 60 h. Finally, in a 5 L bioreactor, titers of 6.18 and 4.97 g/L of tyrosol and HT were achieved for the first time using a temperature-induced strategy. This study presents a method for the modification of microbial chassis for the efficient synthesis of tyrosol and HT.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2294-2304"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126217","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

Host Evolution Improves Genetic Circuit Function in Complex Growth Environments. 宿主进化在复杂生长环境中改善遗传回路功能。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-05-20 DOI: 10.1021/acssynbio.5c00168

Joanna T Zhang, Andrew Lezia, Philip Emmanuele, Muyao Wu, Elina C Olson, Aayush Somani, Adam M Feist, Jeff Hasty

引用次数: 0

Fabrication, Evolution, and Mutual Conversion of d-Fucose-Activatable and -Repressible Acetyltransferase upon Mutations. d-聚焦可激活和可抑制乙酰转移酶在突变中的制造、进化和相互转化。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20 Epub Date: 2025-04-30 DOI: 10.1021/acssynbio.4c00169

Yuki Yanai, Miyu Tsukada, Yuki Kimura, Daisuke Umeno

{"title":"Fabrication, Evolution, and Mutual Conversion of d-Fucose-Activatable and -Repressible Acetyltransferase upon Mutations.","authors":"Yuki Yanai, Miyu Tsukada, Yuki Kimura, Daisuke Umeno","doi":"10.1021/acssynbio.4c00169","DOIUrl":"10.1021/acssynbio.4c00169","url":null,"abstract":"The fusion of different proteins can result in the linkage-dependent emergence of molecular switches. We inserted chloramphenicol acetyltransferase (CAT) from Escherichia coli into a loop of a d-fucose-responsive mutant of transcription factor AraC, using linker libraries with various lengths. We found that on-switches tend to emerge when two proteins are fused with linkers long enough to fill the gap of the distance of residues to be connected, while fusing with short or zero linkers results in the frequent emergence of off-switches. Both types of switches rapidly evolved their switching efficiency upon mutations, establishing the d-fucose-on and -off regulations of CAT activity without disrupting the d-fucose-inducible logic of AraC function. To our surprise, both one-input/two-output split gates thus obtained could be easily interconverted upon mutations. Through mutations, fusion proteins rapidly establish and evolve mutual regulatory relationships with unrelated partner proteins, enabling diverse functional outcomes. Furthermore, random mutagenesis can alter the behavior of these emergent regulatory relationships, such as interconverting the activation or deactivation of the partner protein upon ligand binding, sometimes at a surprisingly high frequency.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"1936-1947"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952398","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

Optimization of a High-Throughput Screen for Monitoring Disease-Associated Protein Misfolding and Aggregation in Bacteria. 细菌中疾病相关蛋白错误折叠和聚集的高通量筛选优化

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.5c00166

Dafni C Delivoria, Eleni Konia, Ilias Matis, Georgios Skretas

{"title":"Optimization of a High-Throughput Screen for Monitoring Disease-Associated Protein Misfolding and Aggregation in Bacteria.","authors":"Dafni C Delivoria, Eleni Konia, Ilias Matis, Georgios Skretas","doi":"10.1021/acssynbio.5c00166","DOIUrl":"10.1021/acssynbio.5c00166","url":null,"abstract":"Protein misfolding and aggregation are central features of a wide range of diseases, including neurodegenerative disorders, systemic amyloidoses, and cancer. The identification of compounds that can modulate protein folding and aggregation is a key step toward developing effective therapies. High-throughput screening methods are essential for efficiently identifying such compounds. In this study, we optimized a previously developed high-throughput genetic screen for monitoring protein misfolding and aggregation in bacteria. This system is based on monitoring the fluorescence of Escherichia coli cells expressing fusions of human misfolding-prone and disease-related proteins (MisPs) with the green fluorescent protein. We systematically tested a variety of experimental conditions, such as overexpression conditions and MisP-GFP fusion formats, to identify key parameters that affect the sensitivity and dynamic range of the assay. Using misfolding-prone, cancer-associated variants of human p53 as a model system, we found that strong overexpression conditions, such as high copy number vectors, strong promoters, high inducer concentrations, and high overexpression temperatures, can yield optimal assay performance. These optimized assay conditions were also validated with additional MisPs, such as the Alzheimer's disease-associated amyloid-β peptide and variants of superoxide dismutase 1 associated with amyotrophic lateral sclerosis. At the same time, we observed that certain conditions, such as inducer concentrations and overexpression temperature, may need to be precisely fine-tuned for each new MisP target to yield optimal assay performance. Our findings provide a framework for standardizing MisP-GFP screening assays, facilitating their broad application in the discovery of therapeutic agents targeting protein misfolding and aggregation.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"2283-2293"},"PeriodicalIF":3.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143950952","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