Synthetic biology (Oxford, England)最新文献_第2页

Navigating the 'moral hazard' argument in synthetic biology's application. 引导合成生物学应用中的 "道德风险 "论点。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-05-23 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae008

Christopher Hunter Lean

引用次数: 0

Screening putative polyester polyurethane degrading enzymes with semi-automated cell-free expression and nitrophenyl probes. 利用半自动无细胞表达和硝基苯探针筛选假定的聚酯聚氨酯降解酶。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-02-13 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae005

Afrin Ahsan, Dominique Wagner, Vanessa A Varaljay, Victor Roman, Nancy Kelley-Loughnane, Nigel F Reuel

{"title":"Screening putative polyester polyurethane degrading enzymes with semi-automated cell-free expression and nitrophenyl probes.","authors":"Afrin Ahsan, Dominique Wagner, Vanessa A Varaljay, Victor Roman, Nancy Kelley-Loughnane, Nigel F Reuel","doi":"10.1093/synbio/ysae005","DOIUrl":"10.1093/synbio/ysae005","url":null,"abstract":"Cell-free expression (CFE) has shown recent utility in prototyping enzymes for discovery efforts. In this work, CFE is demonstrated as an effective tool to screen putative polyester polyurethane degrading enzyme sequences sourced from metagenomic analysis of biofilms prospected on aircraft and vehicles. An automated fluid handler with a controlled temperature block is used to assemble the numerous 30 µL CFE reactions to provide more consistent results over human assembly. In sum, 13 putative hydrolase enzymes from the biofilm organisms as well as a previously verified, polyester-degrading cutinase were expressed using in-house E. coli extract and minimal linear templates. The enzymes were then tested for esterase activity directly in extract using nitrophenyl conjugated substrates, showing highest sensitivity to shorter substrates (4-nitrophenyl hexanoate and 4-nNitrophenyl valerate). This screen identified 10 enzymes with statistically significant activities against these substrates; however, all were lower in measured relative activity, on a CFE volume basis, to the established cutinase control. This approach portends the use of CFE and reporter probes to rapidly prototype, screen and design for synthetic polymer degrading enzymes from environmental consortia. Graphical Abstract.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"9 1","pages":"ysae005"},"PeriodicalIF":2.6,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10898825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Preparing for the future of precision medicine: synthetic cell drug regulation. 为未来的精准医疗做准备：合成细胞药物调控。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-01-27 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae004

Kira Sampson, Carlise Sorenson, Katarzyna P Adamala

引用次数: 0

The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose. 柚皮苷依赖性调节器 FdeR 可用作由柚皮苷和阿拉伯糖控制的 NIMPLY 门。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2024-01-16 eCollection Date: 2024-01-01 DOI: 10.1093/synbio/ysae001

Fernanda Miyuki Kashiwagi, Brenno Wendler Miranda, Emanuel Maltempi de Souza, Marcelo Müller-Santos

{"title":"The naringenin-dependent regulator FdeR can be applied as a NIMPLY gate controlled by naringenin and arabinose.","authors":"Fernanda Miyuki Kashiwagi, Brenno Wendler Miranda, Emanuel Maltempi de Souza, Marcelo Müller-Santos","doi":"10.1093/synbio/ysae001","DOIUrl":"10.1093/synbio/ysae001","url":null,"abstract":"The FdeR regulator has been reported as a transcriptional activator dependent on the interaction with naringenin. Previously, FdeR and its cognate promoter were used to construct naringenin-sensitive sensors, though no correlation was associated between the FdeR level of expression and outputs. Therefore, to understand this correlation, we constructed a circuit with FdeR expression adjusted by the arabinose concentration through an AraC-PBAD system and the FdeR-regulated promoter controlling the expression of GFP. We observed a significant reduction in the activity of the target promoter by increasing FdeR expression, indicating that although FdeR has been primarily classified as a transcriptional activator, it also represses transcription. Leveraging the bifunctional feature of FdeR, acting as both transcriptional activator and repressor, we demonstrated that this genetic circuit, when previously switched on by naringenin, can be switched off by inducing an increased FdeR expression level. This engineered system functioned as a NIMPLY gate, effectively decreasing GFP expression by 50% when arabinose was added without removing naringenin from the medium. Exploiting FdeR versatility, this study demonstrates an innovative application of this transcriptional factor for developing novel NIMPLY gates activated by a molecule with low toxicity and nutraceutical properties that may be important for several applications. Graphical Abstract.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"9 1","pages":"ysae001"},"PeriodicalIF":2.6,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10799723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139514515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell-free expression of RuBisCO for ATP production in the synthetic cells. 在合成细胞中无细胞表达 RuBisCO 以产生 ATP。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2023-12-20 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad016

Shugo Sugii, Katsumi Hagino, Ryo Mizuuchi, Norikazu Ichihashi

引用次数: 0

Special issue: reproducibility in synthetic biology. 特刊:合成生物学的可重复性。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2023-11-16 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad015

Matthew W Lux, Elizabeth A Strychalski, Gary J Vora

引用次数: 0

pBLAM1-x: standardized transposon tools for high-throughput screening. pBLAM1-x:用于高通量筛选的标准化转座子工具。

Synthetic biology (Oxford, England) Pub Date : 2023-06-21 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad012

Lorea Alejaldre, Ana-Mariya Anhel, Ángel Goñi-Moreno

引用次数: 1

Biosynthesis of cannabigerol and cannabigerolic acid: the gateways to further cannabinoid production. 大麻酚和大麻酚酸的生物合成：进一步生产大麻素的途径。

Synthetic biology (Oxford, England) Pub Date : 2023-05-27 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad010

Lewis J Kearsey, Cunyu Yan, Nicole Prandi, Helen S Toogood, Eriko Takano, Nigel S Scrutton

{"title":"Biosynthesis of cannabigerol and cannabigerolic acid: the gateways to further cannabinoid production.","authors":"Lewis J Kearsey, Cunyu Yan, Nicole Prandi, Helen S Toogood, Eriko Takano, Nigel S Scrutton","doi":"10.1093/synbio/ysad010","DOIUrl":"10.1093/synbio/ysad010","url":null,"abstract":"Cannabinoids are a therapeutically valuable class of secondary metabolites with a vast number of substituents. The native cannabinoid biosynthetic pathway of Cannabis sativa generates cannabigerolic acid (CBGA), the common substrate to multiple cannabinoid synthases. The bioactive decarboxylated analog of this compound, cannabigerol (CBG), represents an alternate gateway into the cannabinoid space as a substrate either to non-canonical cannabinoid synthase homologs or to synthetic chemical reactions. Herein, we describe the identification and repurposing of aromatic prenyltransferase (AtaPT), which when coupled with native enzymes of C. sativa can form an Escherichia coli production system for CBGA in cell lysates and CBG in whole cells. Engineering of AtaPT, guided by structural analysis, was performed to enhance its kinetics toward CBGA production for subsequent use in a proof-of-concept lysate system. For the first time, we show a synthetic biology platform for CBG biosynthesis in E. coli cells by employing AtaPT under an optimized microbial system. Our results have therefore set the foundation for sustainable production of well-researched and rarer cannabinoids in an E. coli chassis. Graphical Abstract.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"8 1","pages":"ysad010"},"PeriodicalIF":0.0,"publicationDate":"2023-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10263468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9655827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rewiring cell-free metabolic flux in E. coli lysates using a block-push-pull approach. 使用块推拉方法重新连接大肠杆菌裂解物中的无细胞代谢通量。

Synthetic biology (Oxford, England) Pub Date : 2023-04-17 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad007

Jaime Lorenzo N Dinglasan, Mitchel J Doktycz

{"title":"Rewiring cell-free metabolic flux in E. coli lysates using a block-push-pull approach.","authors":"Jaime Lorenzo N Dinglasan, Mitchel J Doktycz","doi":"10.1093/synbio/ysad007","DOIUrl":"https://doi.org/10.1093/synbio/ysad007","url":null,"abstract":"Cell-free systems can expedite the design and implementation of biomanufacturing processes by bypassing troublesome requirements associated with the use of live cells. In particular, the lack of survival objectives and the open nature of cell-free reactions afford engineering approaches that allow purposeful direction of metabolic flux. The use of lysate-based systems to produce desired small molecules can result in competitive titers and productivities when compared to their cell-based counterparts. However, pathway crosstalk within endogenous lysate metabolism can compromise conversion yields by diverting carbon flow away from desired products. Here, the 'block-push-pull' concept of conventional cell-based metabolic engineering was adapted to develop a cell-free approach that efficiently directs carbon flow in lysates from glucose and toward endogenous ethanol synthesis. The approach is readily adaptable, is relatively rapid and allows for the manipulation of central metabolism in cell extracts. In implementing this approach, a block strategy is first optimized, enabling selective enzyme removal from the lysate to the point of eliminating by-product-forming activity while channeling flux through the target pathway. This is complemented with cell-free metabolic engineering methods that manipulate the lysate proteome and reaction environment to push through bottlenecks and pull flux toward ethanol. The approach incorporating these block, push and pull strategies maximized the glucose-to-ethanol conversion in an Escherichia coli lysate that initially had low ethanologenic potential. A 10-fold improvement in the percent yield is demonstrated. To our knowledge, this is the first report of successfully rewiring lysate carbon flux without source strain optimization and completely transforming the consumed input substrate to a desired output product in a lysate-based, cell-free system.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"8 1","pages":"ysad007"},"PeriodicalIF":0.0,"publicationDate":"2023-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71430011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Functional Synthetic Biology. 功能合成生物学。

IF 2.6

Synthetic biology (Oxford, England) Pub Date : 2023-04-08 eCollection Date: 2023-01-01 DOI: 10.1093/synbio/ysad006

Ibrahim Aldulijan, Jacob Beal, Sonja Billerbeck, Jeff Bouffard, Gaël Chambonnier, Nikolaos Ntelkis, Isaac Guerreiro, Martin Holub, Paul Ross, Vinoo Selvarajah, Noah Sprent, Gonzalo Vidal, Alejandro Vignoni

{"title":"Functional Synthetic Biology.","authors":"Ibrahim Aldulijan, Jacob Beal, Sonja Billerbeck, Jeff Bouffard, Gaël Chambonnier, Nikolaos Ntelkis, Isaac Guerreiro, Martin Holub, Paul Ross, Vinoo Selvarajah, Noah Sprent, Gonzalo Vidal, Alejandro Vignoni","doi":"10.1093/synbio/ysad006","DOIUrl":"10.1093/synbio/ysad006","url":null,"abstract":"Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.","PeriodicalId":74902,"journal":{"name":"Synthetic biology (Oxford, England)","volume":"8 1","pages":"ysad006"},"PeriodicalIF":2.6,"publicationDate":"2023-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10105873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9736864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0