ACS Synthetic Biology最新文献_第3页

GOLDBAR: A Framework for Combinatorial Biological Design. GOLDBAR：组合生物设计框架。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-20 DOI: 10.1021/acssynbio.4c00296

Nicholas Roehner, James Roberts, Andrei Lapets, Dany Gould, Vidya Akavoor, Lucy Qin, D Benjamin Gordon, Christopher Voigt, Douglas Densmore

{"title":"GOLDBAR: A Framework for Combinatorial Biological Design.","authors":"Nicholas Roehner, James Roberts, Andrei Lapets, Dany Gould, Vidya Akavoor, Lucy Qin, D Benjamin Gordon, Christopher Voigt, Douglas Densmore","doi":"10.1021/acssynbio.4c00296","DOIUrl":"10.1021/acssynbio.4c00296","url":null,"abstract":"With the rise of new DNA part libraries and technologies for assembling DNA, synthetic biologists are increasingly constructing and screening combinatorial libraries to optimize their biological designs. As combinatorial libraries are used to generate data on design performance, new rules for composing biological designs will emerge. Most formal frameworks for combinatorial design, however, do not yet support formal comparison of design composition, which is needed to facilitate automated analysis and machine learning in massive biological design spaces. To address this need, we introduce a combinatorial design framework called GOLDBAR. Compared with existing frameworks, GOLDBAR enables synthetic biologists to intersect and merge the rules for entire classes of biological designs to extract common design motifs and infer new ones. Here, we demonstrate the application of GOLDBAR to refine/validate design spaces for TetR-homologue transcriptional logic circuits, verify the assembly of a partial nif gene cluster, and infer novel gene clusters for the biosynthesis of rebeccamycin. We also discuss how GOLDBAR could be used to facilitate grammar-based machine learning in synthetic biology.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142002949","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

Heterologous Expression of Epoxomicin in Escherichia coli. 在大肠杆菌中异源表达环氧霉素。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-08 DOI: 10.1021/acssynbio.4c00430

Sarah R Messenger, David F Ackerley, Mark J Calcott

引用次数: 0

Development of a Signal-integrating Reporter to Monitor Mitochondria-ER Contacts. 开发一种信号整合报告器来监测线粒体-ER 接触。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-20 DOI: 10.1021/acssynbio.4c00098

Zheng Yang, David C Chan

{"title":"Development of a Signal-integrating Reporter to Monitor Mitochondria-ER Contacts.","authors":"Zheng Yang, David C Chan","doi":"10.1021/acssynbio.4c00098","DOIUrl":"10.1021/acssynbio.4c00098","url":null,"abstract":"Mitochondria-endoplasmic reticulum contact sites (MERCS) serve as hotspots for important cellular processes, including calcium homeostasis, phospholipid homeostasis, mitochondria dynamics, and mitochondrial quality control. MERCS reporters based on complementation of green fluorescent proteins (GFP) fragments have been designed to visualize MERCS in real-time, but we find that they do not accurately respond to changes in MERCS content. Here, we utilize split LacZ complementing fragments to develop the first MERCS reporter system (termed SpLacZ-MERCS) that continuously integrates the MERCS information within a cell and generates a fluorescent output. Our system exhibits good organelle targeting, no artifactual tethering, and effective, dynamic tracking of the MERCS level in single cells. The SpLacZ-MERCS reporter was validated by drug treatments and genetic perturbations known to affect mitochondria-ER contacts. The signal-integrating nature of SpLacZ-MERCS may enable systematic identification of genes and drugs that regulate mitochondria-ER interactions. Our successful application of the split LacZ complementation strategy to study MERCS may be extended to study other forms of interorganellar crosstalk.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142002948","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

Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast. 酵母中的基因编码、耐噪音、叶黄素生物传感器

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-28 DOI: 10.1021/acssynbio.4c00186

Patarasuda Chaisupa, Md Mahbubur Rahman, Sherry B Hildreth, Saede Moseley, Chauncey Gatling, Matthew R Bryant, Richard F Helm, R Clay Wright

{"title":"Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast.","authors":"Patarasuda Chaisupa, Md Mahbubur Rahman, Sherry B Hildreth, Saede Moseley, Chauncey Gatling, Matthew R Bryant, Richard F Helm, R Clay Wright","doi":"10.1021/acssynbio.4c00186","DOIUrl":"10.1021/acssynbio.4c00186","url":null,"abstract":"Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142085836","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

Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory 冷泉港实验室合成生物学暑期班十年回顾

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 DOI: 10.1021/acssynbio.4c0027610.1021/acssynbio.4c00276

Karmella A. Haynes*, Lauren B. Andrews, Chase L. Beisel, James Chappell, Christian E. Cuba Samaniego, John E. Dueber, Mary J. Dunlop, Elisa Franco, Julius B. Lucks, Vincent Noireaux, David F. Savage, Pamela A. Silver, Michael Smanski and Eric Young,

{"title":"Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory","authors":"Karmella A. Haynes*, Lauren B. Andrews, Chase L. Beisel, James Chappell, Christian E. Cuba Samaniego, John E. Dueber, Mary J. Dunlop, Elisa Franco, Julius B. Lucks, Vincent Noireaux, David F. Savage, Pamela A. Silver, Michael Smanski and Eric Young, ","doi":"10.1021/acssynbio.4c0027610.1021/acssynbio.4c00276","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00276https://doi.org/10.1021/acssynbio.4c00276","url":null,"abstract":"The Cold Spring Harbor Laboratory (CSHL) Summer Course on Synthetic Biology, established in 2013, has emerged as a premier platform for immersive education and research in this dynamic field. Rooted in CSHL’s rich legacy of biological discovery, the course offers a comprehensive exploration of synthetic biology’s fundamentals and applications. Led by a consortium of faculty from diverse institutions, the course structure seamlessly integrates practical laboratory sessions, exploratory research rotations, and enriching seminars by leaders in the field. Over the years, the curriculum has evolved to cover essential topics such as cell-free transcription–translation, DNA construction, computational modeling of gene circuits, engineered gene regulation, and CRISPR technologies. In this review, we describe the history, development, and structure of the course, and discuss how elements of the course might inform the development of other short courses in synthetic biology. We also demonstrate the course’s impact beyond the lab with a summary of alumni contributions to research, education, and entrepreneurship. Through these efforts, the CSHL Summer Course on Synthetic Biology remains at the forefront of shaping the next generation of synthetic biologists.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acssynbio.4c00276","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142270276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic Engineering of Corynebacterium glutamicum for the High-Level Production of l-Valine under Aerobic Conditions. 谷氨酸棒状杆菌在有氧条件下高水平生产 l-缬氨酸的代谢工程。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-06-30 DOI: 10.1021/acssynbio.4c00278

Feiao Wang, Ningyun Cai, Yanlin Leng, Chen Wu, Yanan Wang, Siyu Tian, Chenglin Zhang, Qingyang Xu, Huadong Peng, Ning Chen, Yanjun Li

{"title":"Metabolic Engineering of Corynebacterium glutamicum for the High-Level Production of l-Valine under Aerobic Conditions.","authors":"Feiao Wang, Ningyun Cai, Yanlin Leng, Chen Wu, Yanan Wang, Siyu Tian, Chenglin Zhang, Qingyang Xu, Huadong Peng, Ning Chen, Yanjun Li","doi":"10.1021/acssynbio.4c00278","DOIUrl":"10.1021/acssynbio.4c00278","url":null,"abstract":"l-Valine, an essential amino acid, serves as a valuable compound in various industries. However, engineering strains with both high yield and purity are yet to be delivered for microbial l-valine production. We engineered a Corynebacterium glutamicum strain capable of highly efficient production of l-valine. We initially introduced an acetohydroxy acid synthase mutant from an industrial l-valine producer and optimized a cofactor-balanced pathway, followed by the activation of the nonphosphoenolpyruvate-dependent carbohydrate phosphotransferase system and the introduction of an exogenous Entner-Doudoroff pathway. Subsequently, we weakened anaplerotic pathways, and attenuated the tricarboxylic acid cycle via start codon substitution in icd, encoding isocitrate dehydrogenase. Finally, to balance bacterial growth and l-valine production, an l-valine biosensor-dependent genetic circuit was established to dynamically repress citrate synthase expression. The engineered strain Val19 produced 103 g/L of l-valine with a high yield of 0.35 g/g glucose and a productivity of 2.67 g/L/h. This represents the highest reported l-valine production in C. glutamicum via direct fermentation and exhibits potential for its industrial-scale production, leveraging the advantages of C. glutamicum over other microbes.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464233","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 Microbial Consortia as Living Materials: Advances and Prospectives. 作为活材料的微生物联合体工程学：进展与展望。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-22 DOI: 10.1021/acssynbio.4c00313

Shuchen Wang, Yuewei Zhan, Xue Jiang, Yong Lai

{"title":"Engineering Microbial Consortia as Living Materials: Advances and Prospectives.","authors":"Shuchen Wang, Yuewei Zhan, Xue Jiang, Yong Lai","doi":"10.1021/acssynbio.4c00313","DOIUrl":"10.1021/acssynbio.4c00313","url":null,"abstract":"The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034488","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

Pathway-Adapted Biosensor for High-Throughput Screening of O-Methyltransferase and its Application in Vanillin Synthesis. 用于高通量筛选 O-甲基转移酶的途径适应型生物传感器及其在香兰素合成中的应用

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-29 DOI: 10.1021/acssynbio.4c00287

Pengyu Dong, Yunjuan Fan, Yi-Xin Huo, Lichao Sun, Shuyuan Guo

{"title":"Pathway-Adapted Biosensor for High-Throughput Screening of O-Methyltransferase and its Application in Vanillin Synthesis.","authors":"Pengyu Dong, Yunjuan Fan, Yi-Xin Huo, Lichao Sun, Shuyuan Guo","doi":"10.1021/acssynbio.4c00287","DOIUrl":"10.1021/acssynbio.4c00287","url":null,"abstract":"Vanillin is a widely used flavoring compound in the food, pharmaceutical, and cosmetics area. However, the biosynthesis of vanillin from low-cost shikimic acid is significantly hindered by the low activity of the rate-limiting enzyme, caffeate O-methyltransferase (COMT). To screen COMT variants with improved conversion rates, we designed a biosensing system that is adaptable to the COMT-mediated vanillin synthetic pathway. Through the evolution of aldehyde transcriptional factor YqhC, we obtained a dual-responsive variant, MuYqhC, which positively responds to the product and negatively responds to the substrate, with no response to intermediates. Using the MuYqhC-based vanillin biosensor, we successfully identified a COMT variant, Mu176, that displayed a 7-fold increase in the conversion rate compared to the wild-type COMT. This variant produced 2.38 mM vanillin from 3 mM protocatechuic acid, achieving a conversion rate of 79.33%. The enhanced activity of Mu176 was attributed to an enlarged binding pocket and strengthened substrate interaction. Applying Mu176 to Bacillus subtilis increased the level of vanillin production from shikimic acid by 2.39-fold. Further optimization of the production chassis, increasing the S-adenosylmethionine supply and the precursor concentration, elevated the vanillin titer to 1 mM, marking the highest level of vanillin production from shikimic acid in Bacillus. Our work highlights the significance of the MuYqhC-based biosensing system and the Mu176 variant in vanillin production.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102144","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

Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle. 天然产品工程合成生物学：跨越发现-设计-建造-测试-学习周期的最新进展。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-20 DOI: 10.1021/acssynbio.4c00391

Jonathan Foldi, Jack A Connolly, Eriko Takano, Rainer Breitling

引用次数: 0

Advanced and Safe Synthetic Microbial Chassis with Orthogonal Translation System Integration. 集成正交翻译系统的先进安全合成微生物底盘。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-09-20 Epub Date: 2024-08-16 DOI: 10.1021/acssynbio.4c00437

Hamid Reza Karbalaei-Heidari, Nediljko Budisa

{"title":"Advanced and Safe Synthetic Microbial Chassis with Orthogonal Translation System Integration.","authors":"Hamid Reza Karbalaei-Heidari, Nediljko Budisa","doi":"10.1021/acssynbio.4c00437","DOIUrl":"10.1021/acssynbio.4c00437","url":null,"abstract":"Through the use of CRISPR-assisted transposition, we have engineered a safe Escherichia coli chassis that integrates an orthogonal translation system (OTS) directly into the chromosome. This approach circumvents the limitations and genetic instability associated with conventional plasmid vectors. Precision in genome modification is crucial for the top-down creation of synthetic cells, especially in the orthogonalization of vital cellular processes, such as metabolism and protein translation. Here, we targeted multiple loci in the E. coli chromosome to integrate the OTS simultaneously, creating a synthetic auxotrophic chassis with an altered genetic code to establish a reliable, robust, and safe synthetic protein producer. Our OTS-integrated chassis enabled the site-specific incorporation of m-oNB-Dopa through in-frame amber stop codon readthrough. This allowed for the expression of advanced underwater bioglues containing Dopa-Lysine motifs, which are crucial for wound healing and tissue regeneration. Additionally, we have enhanced the expression process by incorporating scaffold-stabilizing fluoroprolines into bioglues, utilizing our chassis, which has been modified through metabolic engineering (i.e., by introducing proline auxotrophy). We also engineered a synthetic auxotroph reliant on caged Dopa, creating a genetic barrier (genetic firewall) between the synthetic cells and their surroundings, thereby boosting their stability and safety.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992181","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