ACS Synthetic Biology最新文献_第3页

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20

Junqi Zhang, Yuanxiu Li, Wenjing Lv, Zixuan You, Huan Yu, Baocai Zhang, Qijing Liu, Jing Zou, Tao Chen, Feng Li* and Hao Song*,

引用次数: 0

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20

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

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IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20

引用次数: 0

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20

Matthew T. Fernez, Shanthi Hegde, Justin A. Hayes, Kathryn O. Hoyt, Rebecca L. Carrier and Benjamin M. Woolston*,

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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

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

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

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2025-06-20

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 and José I. Jiménez*,

引用次数: 0