ACS Synthetic Biology最新文献_第3页

Light-Induced Nanobody-Mediated Targeted Protein Degradation for Metabolic Flux Control. 光诱导纳米抗体介导的靶向蛋白质降解用于代谢通量控制

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-11 DOI: 10.1021/acssynbio.4c00552

Allison Y Tang, Seyi Jung, César Carrasco-López, José L Avalos

引用次数: 0

Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology. 可产生羟色胺的细菌可调节宿主肠道生理机能

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-27 DOI: 10.1021/acssynbio.4c00453

Chrystal F Mavros, Mareike Bongers, Frederik B F Neergaard, Frank Cusimano, Yiwei Sun, Andrew Kaufman, Miles Richardson, Susanne Kammler, Mette Kristensen, Morten O A Sommer, Harris H Wang

引用次数: 0

De Novo Biosynthesis of a Polyene-Type Ginsenoside Precursor Dammaradienol in Saccharomyces cerevisiae. 在酿酒酵母中从头合成多烯型人参皂苷前体达玛二烯醇

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-20 DOI: 10.1021/acssynbio.4c00396

Yuhong Gan, Zhengping Li, Baolian Fan, Zhongju Ji, Lu Yang, Yuhong Wu, Qiongyu Ye, Aijia Ji, Zhongqiu Liu, Lixin Duan

{"title":"De Novo Biosynthesis of a Polyene-Type Ginsenoside Precursor Dammaradienol in Saccharomyces cerevisiae.","authors":"Yuhong Gan, Zhengping Li, Baolian Fan, Zhongju Ji, Lu Yang, Yuhong Wu, Qiongyu Ye, Aijia Ji, Zhongqiu Liu, Lixin Duan","doi":"10.1021/acssynbio.4c00396","DOIUrl":"10.1021/acssynbio.4c00396","url":null,"abstract":"Typical dammarane-type ginsenosides are well-known tetracyclic triterpenoids with significant pharmacological effects including antitumor, cardiovascular protection, and neuroprotection. Polyene-type ginsenosides exhibit stronger biological activities than common ginsenosides; however, their contents are low, and most are converted from ginsenosides through a series of processing steps, resulting in higher preparation costs. In this study, a dammaradienol synthase, AarOSC20433, was identified for the first time from Artemisia argyi H. Lév. & Vaniot (A. argyi). The high-yielding squalene strain constructed in this study was used as the chassis strain. Yeast heterologous biosynthesis of the polyene-type ginsenoside precursor dammaradienol was achieved via metabolic engineering strategies, including optimization of the terpene supply, increase in copy number of AarOSC20433, and rational enzyme design. Eventually, through replenishment and batch fermentation, the titer of dammaradienol reached 1.037 g/L (4.3 mg/L/OD), laying a solid foundation for the construction of a polyene-type ginsenoside cell factory.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4015-4026"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680309","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

Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline. 翻译增强型新生 SKIK 肽对含有连续脯氨酸的停滞肽的影响

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-21 DOI: 10.1021/acssynbio.4c00221

Yuma Nishikawa, Riko Fujikawa, Hideo Nakano, Takashi Kanamori, Teruyo Ojima-Kato

{"title":"Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline.","authors":"Yuma Nishikawa, Riko Fujikawa, Hideo Nakano, Takashi Kanamori, Teruyo Ojima-Kato","doi":"10.1021/acssynbio.4c00221","DOIUrl":"10.1021/acssynbio.4c00221","url":null,"abstract":"Ribosome arrest peptides (RAPs) such as the SecM arrest peptide (SecM AP: FSTPVWISQAQGIRAGP) and WPPP with consecutive Pro residues are known to induce translational stalling in Escherichia coli. We demonstrate that the translation-enhancing SKIK peptide tag, which consists of four amino acid residues Ser-Lys-Ile-Lys, effectively alleviates translational arrest caused by WPPP. Moreover, the proximity between SKIK and WPPP significantly influences the extent of this alleviation, observed in both PURE cell-free protein synthesis and in vivo protein production systems, resulting in a substantial increase in the yield of proteins containing such RAPs. Furthermore, we unveil that nascent SKIK peptide tag and translation elongation factor P (EF-P) alleviate ribosome stalling in consecutive-Pro-rich protein to synergistically promote translation. A kinetic analysis based on the generation of superfolder green fluorescent protein under in vitro translation reaction reveals that the ribosome turnover is enhanced by more than 10-fold when the SKIK peptide tag is positioned immediately upstream of the SecM AP sequence. Our findings provide valuable insights into optimizing protein production processes, which are essential for advancing synthetic biology applications.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3908-3916"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685398","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 a Silk Protein-Mediated Customizable Compartment for Modular Metabolic Synthesis.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-12-04 DOI: 10.1021/acssynbio.4c00629

Mengqi Ji, Buhan Yao, Jingyu Zhou, Yongzhong Wang, Qiang Ding

{"title":"Engineering a Silk Protein-Mediated Customizable Compartment for Modular Metabolic Synthesis.","authors":"Mengqi Ji, Buhan Yao, Jingyu Zhou, Yongzhong Wang, Qiang Ding","doi":"10.1021/acssynbio.4c00629","DOIUrl":"10.1021/acssynbio.4c00629","url":null,"abstract":"Microbial cell factories provide a nontoxic, economical way for the synthesis of various chemicals and drugs, garnering significant attention from researchers. However, excessive dispersion of enzymes and accumulation of intermediate metabolites in the production process will weaken the reaction efficiency of the pathway enzyme. In this study, a cellular compartment was constructed to isolate the enzyme reaction space and optimize the modular metabolic synthesis. First, a special spider silk protein was designed and constructed to form protein condensates in microbial cells, and its synthetic microcompartment effects were investigated. Second, the interaction of short peptide pairs or direct fusion based on the silk protein was used to recruit a variety of enzymes to improve the efficiency of enzyme catalysis. Third, the 2'-fucosyllactose (2'-FL) de novo synthesis pathway and its modular optimization were carried out to verify the mode. Finally, a synthetic compartment was introduced into the pathway to directly aggregate the 2'-FL synthesis pathway, thus obtaining synthetic-compartment-mediated multienzyme aggregates. The experimental results showed that the titer of 2'-FL was significantly improved compared with those of wild-type and modular-optimized free enzymes. The utilization of this cell microcompartment offers a novel avenue for the aggregation of diverse enzymes, thereby offering an innovative approach for enhancing the efficiency of the microbial modular metabolic pathway.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4180-4190"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764677","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 Ecosystems: From the Test Tube to the Biosphere. 合成生态系统：从试管到生物圈。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-21 DOI: 10.1021/acssynbio.4c00384

Ricard Solé, Victor Maull, Daniel R Amor, Jordi Pla Mauri, Conde-Pueyo Núria

{"title":"Synthetic Ecosystems: From the Test Tube to the Biosphere.","authors":"Ricard Solé, Victor Maull, Daniel R Amor, Jordi Pla Mauri, Conde-Pueyo Núria","doi":"10.1021/acssynbio.4c00384","DOIUrl":"10.1021/acssynbio.4c00384","url":null,"abstract":"The study of ecosystems, both natural and artificial, has historically been mediated by population dynamics theories. In this framework, quantifying population numbers and related variables (associated with metabolism or biological-environmental interactions) plays a central role in measuring and predicting system-level properties. As we move toward advanced technological engineering of cells and organisms, the possibility of bioengineering ecosystems (from the gut microbiome to wildlands) opens several questions that will require quantitative models to find answers. Here, we present a comprehensive survey of quantitative modeling approaches for managing three kinds of synthetic ecosystems, sharing the presence of engineered strains. These include test tube examples of ecosystems hosting a relatively low number of interacting species, mesoscale closed ecosystems (or ecospheres), and macro-scale, engineered ecosystems. The potential outcomes of synthetic ecosystem designs and their limits will be relevant to different disciplines, including biomedical engineering, astrobiology, space exploration and fighting climate change impacts on endangered ecosystems. We propose a space of possible ecosystems that captures this broad range of scenarios and a tentative roadmap for open problems and further exploration.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"3812-3826"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680312","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

Advancements in Biological Conversion of C1 Feedstocks: Sustainable Bioproduction and Environmental Solutions.

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-29 DOI: 10.1021/acssynbio.4c00519

Wooyoung Park, Seungwoo Cha, Ji-Sook Hahn

引用次数: 0

GRACE: Generative Redesign in Artificial Computational Enzymology. GRACE：人工计算酶学中的生成再设计。

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-08 DOI: 10.1021/acssynbio.4c00624

Ruei-En Hu, Chi-Hua Yu, I-Son Ng

引用次数: 0

Optogenetic Control of Phosphate-Responsive Genes Using Single-Component Fusion Proteins in Saccharomyces cerevisiae. 在酿酒酵母中使用单组分融合蛋白对磷酸响应基因进行光遗传学控制

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-12 DOI: 10.1021/acssynbio.4c00529

Matthew M Cleere, Kevin H Gardner

{"title":"Optogenetic Control of Phosphate-Responsive Genes Using Single-Component Fusion Proteins in Saccharomyces cerevisiae.","authors":"Matthew M Cleere, Kevin H Gardner","doi":"10.1021/acssynbio.4c00529","DOIUrl":"10.1021/acssynbio.4c00529","url":null,"abstract":"Blue light illumination can be detected by light-oxygen-voltage (LOV) photosensing proteins and translated into a range of biochemical responses, facilitating the generation of novel optogenetic tools to control cellular function. Here, we develop new variants of our previously described VP-EL222 light-dependent transcription factor and apply them to study the phosphate-responsive signaling (PHO) pathway in the budding yeast Saccharomyces cerevisiae, exemplifying the utilities of these new tools. Focusing first on the VP-EL222 protein itself, we quantified the tunability of gene expression as a function of light intensity and duration and demonstrated that this system can tolerate the addition of substantially larger effector domains without impacting function. We further demonstrated the utility of several EL222-driven transcriptional controllers in both plasmid and genomic settings, using the PHO5 and PHO84 promoters in their native chromosomal contexts as examples. These studies highlight the utility of light-controlled gene activation using EL222 tethered to either artificial transcription domains or yeast activator proteins (Pho4). Similarly, we demonstrate the ability to optogenetically repress gene expression with EL222 fused to the yeast Ume6 protein. We finally investigated the effects of moving EL222 recruitment sites to different locations within the PHO5 and PHO84 promoters, as well as determining how this artificial light-controlled regulation could be integrated with the native controls dependent on inorganic phosphate (Pi) availability. Taken together, our work expands the applicability of these versatile optogenetic tools in the types of functionalities that they can deliver and the biological questions that can be probed.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4085-4098"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612583","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 Eukaryote-Featured Membrane Phospholipid Enhances Bacterial Formaldehyde Tolerance and Assimilation of One-Carbon Feedstocks. 真核生物膜磷脂可增强细菌耐受甲醛和吸收一碳原料的能力

IF 3.7 2区生物学

ACS Synthetic Biology Pub Date : 2024-12-20 Epub Date: 2024-11-20 DOI: 10.1021/acssynbio.4c00499

MengKun Li, Wenjie Sun, Xin Wang, Kequan Chen, Yan Feng, Zaigao Tan

{"title":"A Eukaryote-Featured Membrane Phospholipid Enhances Bacterial Formaldehyde Tolerance and Assimilation of One-Carbon Feedstocks.","authors":"MengKun Li, Wenjie Sun, Xin Wang, Kequan Chen, Yan Feng, Zaigao Tan","doi":"10.1021/acssynbio.4c00499","DOIUrl":"10.1021/acssynbio.4c00499","url":null,"abstract":"Efficient bioassimilation of one-carbon (C1) feedstocks is often hindered by the toxicity of C1 substrates and/or intermediates. We compared the toxicity of several common C1 substrates/intermediates and found that formaldehyde imposes the highest toxicity on the representative bacterium Escherichia coli. Besides causing chromosomal DNA and protein damage effects, here, we revealed that formaldehyde greatly impairs cell membranes. To this end, here, we sought to remodel the cell membrane of E. coli by introducing a non-native, eukaryote-featured membrane phospholipid composition, phosphatidylcholine (PC). This engineered E. coli strain exhibited significantly increased membrane integrity, resulting in enhanced formaldehyde tolerance. When applied to C1 assimilation, the PC-harboring E. coli consumed up to 4.7 g/L methanol, which is 23-fold higher than that of the control strain (0.2 g/L). In summary, the present study highlights the detrimental impact of formaldehyde-induced membrane damage and thus underscores the significance of membrane remodeling in enhancing formaldehyde tolerance and facilitating the assimilation of C1 substrates.","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":"4074-4084"},"PeriodicalIF":3.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674584","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