ACS Synthetic Biology最新文献_第10页

Design of a Genetically Programmable and Customizable Protein Scaffolding System for the Hierarchical Assembly of Robust, Functional Macroscale Materials. 设计一种基因可编程和可定制的蛋白质支架系统，用于分层组装稳健的功能性宏观材料。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-31 DOI: 10.1021/acssynbio.4c00587

Ruijie Zhang, Sun-Young Kang, François Gaascht, Eliana L Peña, Claudia Schmidt-Dannert

{"title":"Design of a Genetically Programmable and Customizable Protein Scaffolding System for the Hierarchical Assembly of Robust, Functional Macroscale Materials.","authors":"Ruijie Zhang, Sun-Young Kang, François Gaascht, Eliana L Peña, Claudia Schmidt-Dannert","doi":"10.1021/acssynbio.4c00587","DOIUrl":"10.1021/acssynbio.4c00587","url":null,"abstract":"Inspired by the properties of natural protein-based biomaterials, protein nanomaterials are increasingly designed with natural or engineered peptides or with protein building blocks. Few examples describe the design of functional protein-based materials for biotechnological applications that can be readily manufactured, are amenable to functionalization, and exhibit robust assembly properties for macroscale material formation. Here, we designed a protein-scaffolding system that self-assembles into robust, macroscale materials suitable for in vitro cell-free applications. By controlling the coexpression in Escherichia coli of self-assembling scaffold building blocks with and without modifications for covalent attachment of cross-linking cargo proteins, hybrid scaffolds with spatially organized conjugation sites are overproduced that can be readily isolated. Cargo proteins, including enzymes, are rapidly cross-linked onto scaffolds for the formation of functional materials. We show that these materials can be used for the in vitro operation of a coimmobilized two-enzyme reaction and that the protein material can be recovered and reused. We believe that this work will provide a versatile platform for the design and scalable production of functional materials with customizable properties and the robustness required for biotechnological applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3724-3745"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542841","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

Critical Assessment of Protein Engineering (CAPE): A Student Challenge on the Cloud. 蛋白质工程批判性评估 (CAPE)：云上的学生挑战赛。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-11-07 DOI: 10.1021/acssynbio.4c00588

Lihao Fu, Yuan Gao, Yongcan Chen, Yanjing Wang, Xiaoting Fang, Shujun Tian, Hao Dong, Yijian Zhang, Zichuan Chen, Zechen Wang, Shantong Hu, Xiao Yi, Tong Si

{"title":"Critical Assessment of Protein Engineering (CAPE): A Student Challenge on the Cloud.","authors":"Lihao Fu, Yuan Gao, Yongcan Chen, Yanjing Wang, Xiaoting Fang, Shujun Tian, Hao Dong, Yijian Zhang, Zichuan Chen, Zechen Wang, Shantong Hu, Xiao Yi, Tong Si","doi":"10.1021/acssynbio.4c00588","DOIUrl":"10.1021/acssynbio.4c00588","url":null,"abstract":"The success of AlphaFold in protein structure prediction highlights the power of data-driven approaches in scientific research. However, developing machine learning models to design and engineer proteins with desirable functions is hampered by limited access to high-quality data sets and experimental feedback. The Critical Assessment of Protein Engineering (CAPE) challenge addresses these issues through a student-focused competition, utilizing cloud computing and biofoundries to lower barriers to entry. CAPE serves as an open platform for community learning, where mutant data sets and design algorithms from past contestants help improve overall performance in subsequent rounds. Through two competition rounds, student participants collectively designed >1500 new mutant sequences, with the best-performing variants exhibiting catalytic activity up to 5-fold higher than the wild-type parent. We envision CAPE as a collaborative platform to engage young researchers and promote computational protein engineering.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3782-3787"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11574941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589283","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

Precision Transcriptome Editing. 精确转录组编辑。

IF 4.3 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-22 DOI: 10.1021/acssynbio.4c00183

Crystal Chen, Lei S Qi

引用次数: 0

Versatile Dual Reporter to Identify Ribosome Pausing Motifs Alleviated by Translation Elongation Factor P. 多用途双报告器可识别由翻译延伸因子 P 缓解的核糖体停顿位点

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-19 DOI: 10.1021/acssynbio.4c00534

Urte Tomasiunaite, Tess Brewer, Korinna Burdack, Sophie Brameyer, Kirsten Jung

{"title":"Versatile Dual Reporter to Identify Ribosome Pausing Motifs Alleviated by Translation Elongation Factor P.","authors":"Urte Tomasiunaite, Tess Brewer, Korinna Burdack, Sophie Brameyer, Kirsten Jung","doi":"10.1021/acssynbio.4c00534","DOIUrl":"10.1021/acssynbio.4c00534","url":null,"abstract":"Protein synthesis is influenced by the chemical and structural properties of the amino acids incorporated into the polypeptide chain. Motifs containing consecutive prolines can slow the translation speed and cause ribosome stalling. Translation elongation factor P (EF-P) facilitates peptide bond formation in these motifs, thereby alleviating stalled ribosomes and restoring the regular translational speed. Ribosome pausing at various polyproline motifs has been intensively studied using a range of sophisticated techniques, including ribosome profiling, proteomics, and in vivo screening, with reporters incorporated into the chromosome. However, the full spectrum of motifs that cause translational pausing in Escherichia coli has not yet been identified. Here, we describe a plasmid-based dual reporter for rapid assessment of pausing motifs. This reporter contains two coupled genes encoding mScarlet-I and chloramphenicol acetyltransferase to screen motif libraries based on both bacterial fluorescence and survival. In combination with a diprolyl motif library, we used this reporter to reveal motifs of different pausing strengths in an E. coli strain lacking efp. Subsequently, we used the reporter for a high-throughput screen of four motif libraries, with and without prolines at different positions, sorted by fluorescence-associated cell sorting (FACS) and identify new motifs that influence the translational efficiency of the fluorophore. Our study provides an in vivo platform for rapid screening of amino acid motifs that affect translational efficiencies.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3698-3710"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453381","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

De Novo Biosynthesis of a Bioactive Meroterpene Bakuchiol in Yeast. 酵母中生物活性 Meroterpene Bakuchiol 的新生物合成。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-30 DOI: 10.1021/acssynbio.4c00416

Yi-Lei Zheng, Ye Xu, Yan-Qiu Liu, Qing-Wei Zhao, Yong-Quan Li

{"title":"De Novo Biosynthesis of a Bioactive Meroterpene Bakuchiol in Yeast.","authors":"Yi-Lei Zheng, Ye Xu, Yan-Qiu Liu, Qing-Wei Zhao, Yong-Quan Li","doi":"10.1021/acssynbio.4c00416","DOIUrl":"10.1021/acssynbio.4c00416","url":null,"abstract":"Bakuchiol (BAK), a specialized meroterpene, is known for its valuable biological properties and has recently gained prominence in cosmetology for its retinol-like functionality. However, low abundance in natural sources leads to environmentally unfriendly and unsustainable practices associated with crop-based manufacturing and chemical synthesis. Here, we identified a prenyltransferase (PT) from Psoralea corylifolia that catalyzes the reverse geranylation of a nonaromatic carbon in para-coumaric acid (p-CA), coupled with a decarboxylation step to form BAK. Given that the biosynthesis pathway of BAK is well elucidated, we engineered Saccharomyces cerevisiae to produce BAK, starting from glucose. To enhance the titer of BAK, we employed a multifaceted approach that included increasing the supply of precursors, balancing the fluxes in the two parallel biosynthetic pathways, engineering of prenyltransferase, and fusing enzymes. Consequently, the engineered yeast strains showed a marked improvement of 117.3-fold in BAK production, reaching a titer of 9.28 mg/L from glucose. Our work provides a viable approach for the sustainable microbial production of complex natural meroterpenes.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3600-3608"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542792","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

Formaldehyde: An Essential Intermediate for C1 Metabolism and Bioconversion. 甲醛：C1 代谢和生物转化的重要中间体。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-12 DOI: 10.1021/acssynbio.4c00454

Mengshi Jia, Mengge Liu, Jiawen Li, Wankui Jiang, Fengxue Xin, Wenming Zhang, Yujia Jiang, Min Jiang

引用次数: 0

Rational and Semirational Approaches for Engineering Salicylate Production in Escherichia coli. 大肠杆菌水杨酸盐生产工程的合理和半合理方法。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-25 DOI: 10.1021/acssynbio.4c00366

Chenghu Chen, Cong Gao, Guipeng Hu, Wanqing Wei, Xiaoge Wang, Jian Wen, Xiulai Chen, Liming Liu, Wei Song, Jing Wu

{"title":"Rational and Semirational Approaches for Engineering Salicylate Production in Escherichia coli.","authors":"Chenghu Chen, Cong Gao, Guipeng Hu, Wanqing Wei, Xiaoge Wang, Jian Wen, Xiulai Chen, Liming Liu, Wei Song, Jing Wu","doi":"10.1021/acssynbio.4c00366","DOIUrl":"10.1021/acssynbio.4c00366","url":null,"abstract":"Salicylate plays a pivotal role as a pharmaceutical intermediate in drugs, such as aspirin and lamivudine. The low catalytic efficiency of key enzymes and the inherent toxicity of salicylates to cells pose significant challenges to large-scale microbial production. In this study, we introduced the salicylate synthase Irp9 into an l-phenylalanine-producing Escherichia coli, constructing the shortest salicylate biosynthetic pathway. Subsequent protein engineering increased the catalytic efficiency of Irp9 by 33.5%. Furthermore, by integrating adaptive evolution with transcriptome analysis, we elucidated the crucial mechanism of efflux proteins in salicylate tolerance. The elucidation of this mechanism guided us in the targeted modification of these transport proteins, achieving a reported maximum level of 3.72 g/L of salicylate in a shake flask. This study highlights the importance of efflux proteins for enhancing the productivity of microbial cell factories in salicylate production, which also holds potential for application in the green synthesis of other phenolic acids.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3563-3575"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491078","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

Ribozyme-Mediated Gene-Fragment Complementation for Nondestructive Reporting of DNA Transfer within Soil. 以核酸酶为介导的基因片段互补，用于无损地报告 DNA 在土壤中的转移。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-08-15 DOI: 10.1021/acssynbio.4c00264

Malyn A Selinidis, Andrew C Corliss, James Chappell, Jonathan J Silberg

{"title":"Ribozyme-Mediated Gene-Fragment Complementation for Nondestructive Reporting of DNA Transfer within Soil.","authors":"Malyn A Selinidis, Andrew C Corliss, James Chappell, Jonathan J Silberg","doi":"10.1021/acssynbio.4c00264","DOIUrl":"10.1021/acssynbio.4c00264","url":null,"abstract":"Enzymes that produce volatile metabolites can be coded into genetic circuits to report nondisruptively on microbial behaviors in hard-to-image soils. However, these enzyme reporters remain challenging to apply in gene transfer studies due to leaky off states that can lead to false positives. To overcome this problem, we designed a reporter that uses ribozyme-mediated gene-fragment complementation of a methyl halide transferase (MHT) to regulate the synthesis of methyl halide gases. We split the mht gene into two nonfunctional fragments and attached these to a pair of splicing ribozyme fragments. While the individual mht-ribozyme fragments did not produce methyl halides when transcribed alone in Escherichia coli, coexpression resulted in a spliced transcript that translated the MHT reporter. When cells containing one mht-ribozyme fragment transcribed from a mobile plasmid were mixed with cells that transcribed the second mht-ribozyme fragment, methyl halides were only detected following rare conjugation events. When conjugation was performed in soil, it led to a 16-fold increase in methyl halides in the soil headspace. These findings show how ribozyme-mediated gene-fragment complementation can achieve tight control of protein reporter production, a level of control that will be critical for monitoring the effects of soil conditions on gene transfer and the fidelity of biocontainment measures developed for environmental applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3539-3547"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981169","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

A Tunable Long Duration Pulse Generation Circuit in Mammalian Cells. 哺乳动物细胞中的可调长脉冲发生电路

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-17 DOI: 10.1021/acssynbio.4c00368

Noreen Wauford, Georg Wachter, Katherine Kiwimagi, Ron Weiss

{"title":"A Tunable Long Duration Pulse Generation Circuit in Mammalian Cells.","authors":"Noreen Wauford, Georg Wachter, Katherine Kiwimagi, Ron Weiss","doi":"10.1021/acssynbio.4c00368","DOIUrl":"10.1021/acssynbio.4c00368","url":null,"abstract":"Pulse generator circuits based on incoherent feed-forward logic have been developed in bacterial, yeast, and mammalian systems but are typically limited to production of short pulses lasting less than 1 day. To generate longer-lasting pulses, we introduce a feedback-based topology that induces multiday pulsatile gene expression with tunable duration and amplitude in mammalian cells. We constructed the circuit using the PERSIST platform, which consists of entirely post-transcriptional logic, because our experience suggests that this approach may attenuate long-term epigenetic silencing. To enable external regulation of PERSIST regulatory elements, we engineered inducer-stabilized CRISPR endoRNases that respond to FDA-approved drugs, generating small molecule responses with greater than 20-fold change. These inducer-responsive proteins were connected to a two-state cross-repression positive feedback topology to generate the pulse generator circuit architecture. We then optimized circuit design through chromosomal integration of circuit components at varying stoichiometries, resulting in a small library of circuits displaying tunable pulses lasting between two and 6 days in response to a single 24 h input of inducer. We expect that the small molecule-stabilized PERSIST proteins developed will serve as valuable components in the toolbox for post-transcriptional gene circuit development and that tunable post-transcriptional pulse generator circuits in mammalian cells will enable study of endogenous hysteretic gene networks and support advances in cell therapies and organoid engineering.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3576-3586"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453362","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

Dual-Plasmid Mini-Tn5 System to Stably Integrate Multicopy of Target Genes in Escherichia coli. 在大肠杆菌中稳定整合多拷贝目标基因的双质粒 Mini-Tn5 系统

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-11-15 Epub Date: 2024-10-17 DOI: 10.1021/acssynbio.4c00140

Menghui Liu, Wei Ge, Guomei Zhong, Yuqing Yang, Luying Xun, Yongzhen Xia

{"title":"Dual-Plasmid Mini-Tn5 System to Stably Integrate Multicopy of Target Genes in Escherichia coli.","authors":"Menghui Liu, Wei Ge, Guomei Zhong, Yuqing Yang, Luying Xun, Yongzhen Xia","doi":"10.1021/acssynbio.4c00140","DOIUrl":"10.1021/acssynbio.4c00140","url":null,"abstract":"The efficiency of valuable metabolite production by engineered microorganisms underscores the importance of stable and controllable gene expression. While plasmid-based methods offer flexibility, integrating genes into host chromosomes can establish stability without selection pressure. However, achieving site-directed multicopy integration presents challenges, including site selection and stability. We introduced a stable multicopy integration method by using a novel dual-plasmid mini-Tn5 system to insert genes into Escherichia coli's genome. The gene of interest was combined with a removable antibiotic resistance gene. After the selection of bacteria with inserted genes, the antibiotic resistance gene was removed. Optimizations yielded an integration efficiency of approximately 5.5 × 10-3 per recipient cell in a single round. Six rounds of integration resulted in 19 and 5 copies of the egfp gene in the RecA+ strain MG1655 and the RecA- strain XL1-Blue MRF', respectively. Additionally, we integrated a polyhydroxybutyrate (PHB) synthesis gene cluster into E. coli MG1655, yielding an 8-copy integration strain producing more PHB than strains with the cluster on a high-copy plasmid. The method was efficient in generating gene insertions in various E. coli strains, and the inserted genes were stable after extended culture. This stable, high-copy integration tool offers potential for diverse applications in synthetic biology.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3523-3538"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453376","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