Synthetic and Systems Biotechnology最新文献_第5页

Metabolic engineering Saccharomyces cerevisiae for de novo biosynthesis of hydroxycinnamoyl glycerols 代谢工程羟基肉桂酰甘油的酿酒酵母新生物合成

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-07-17 DOI: 10.1016/j.synbio.2025.07.005

Haiyan Zou, Chuanguang Xiao, Shujuan Zhao

{"title":"Metabolic engineering Saccharomyces cerevisiae for de novo biosynthesis of hydroxycinnamoyl glycerols","authors":"Haiyan Zou, Chuanguang Xiao, Shujuan Zhao","doi":"10.1016/j.synbio.2025.07.005","DOIUrl":"10.1016/j.synbio.2025.07.005","url":null,"abstract":"<div><div>Hydroxycinnamoyl glycerols (HCGs) are a class of bioconjugates characterized by the esterification of hydroxycinnamic acids with glycerol. Owing to their diverse biological activities, HCGs are considered high-value materials with potential applications in the food, pharmaceutical, and cosmetics industries. In this study, a <em>de novo</em> biosynthetic pathway of HCGs was constructed by integrating a <em>p</em>-coumaric acid-producing module and a 4-coumarate:coenzyme A ligase - hydroxycinnamoyltransferase (4CL-HCT) module into the genome of <em>Saccharomyces cerevisiae</em>. Through optimization of the primary metabolic pathway, fine-tuning of the shikimate pathway, and strategic selection of integration sites, the upstream metabolic flux in the <em>S. cerevisiae</em> strain was engineering to enhance the availability of <span>l</span>-tyrosine and <span>l</span>-phenylalanine precursors, as well as acetyl-coenzyme A (acetyl-CoA) and adenosine triphosphate (ATP) supply. As a result, the final engineered <em>S. cerevisiae</em> strain produced 1-<em>O</em>-<em>p</em>-coumaroylglycerol (1-OPCG) at a titer of 8.49 ± 2.29 μg/L in shake-flask fermentation. The strategies employed in this study provide a robust foundation for the synthesis of other HCGs.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1257-1266"},"PeriodicalIF":4.4,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144704843","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

Enzyme and cofactor engineering to increase d-xylonate dehydratase activity for improved d-1,2,4-butanetriol production from d-xylose 提高d-木糖酸脱水酶活性以提高d-木糖生产d-1,2,4-丁三醇的酶和辅助因子工程

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-07-08 DOI: 10.1016/j.synbio.2025.07.003

Jingwen Chen, Zhangyu Liu, Dandan Mai, Sheng Xu, Xin Wang, Kequan Chen

{"title":"Enzyme and cofactor engineering to increase d-xylonate dehydratase activity for improved d-1,2,4-butanetriol production from d-xylose","authors":"Jingwen Chen, Zhangyu Liu, Dandan Mai, Sheng Xu, Xin Wang, Kequan Chen","doi":"10.1016/j.synbio.2025.07.003","DOIUrl":"10.1016/j.synbio.2025.07.003","url":null,"abstract":"<div><div>d-1,2,4-Butanetriol (BTO), a C4 platform compound, is widely used in fields such as military and pharmaceuticals. Biosynthesis of d-1,2,4-BTO from lignocellulose-derived <span>d</span>-xylose presents a promising production route. However, the low catalytic activity of <span>d</span>-xylonate dehydratase leading to the accumulation of <span>d</span>-xylonic acid remains a key bottleneck for the efficient production of d-1,2,4-BTO. In this study, we aimed to enhance the catalytic activity of <span>d</span>-xylonate dehydratase through an integrated enzyme and cofactor engineering approach. Firstly, we evolved the <span>d</span>-xylonate dehydratase YjhG by using both random mutagenesis and site-directed saturation mutagenesis. Among the generated variants, YjhG<sup>T325F</sup> showed an 1.82-fold increase in <span>d</span>-xylonic acid consumption compared to the wild-type enzyme. When introduced into the producing strain, this variant increased d-1,2,4-BTO production by 1.34-fold compared to the original strain. Further enhancement was achieved by modifying the iron-sulfur [Fe–S] cluster synthesis system, which was critical for <span>d</span>-xylonate dehydratase activity. We systematically evaluated three [Fe–S] assembly systems, including SUF (encoded by <em>sufABCDSE</em>), ISC (encoded by <em>iscSUA-hscBA-fdx</em>), and CSD (encoded by <em>csdAE</em>). Comparative analysis revealed that the overexpression of SUF system conferred the highest catalytic efficiency of YjhG. The recombinant strain of BT-YjhG<sup>T325F</sup>-SUF produced 10.36 g/L of d-1,2,4-BTO from <span>d</span>-xylose, achieving a molar yield of 73.6 %, which was 1.88-fold that of the original strain. This study provided a robust foundation for high-efficiency d-1,2,4-BTO production through enzyme and cofactor engineering.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1234-1241"},"PeriodicalIF":4.4,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144694925","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 multifunctional switch for label-free CRISPR/Cas12a sensor with self-driven amplification 一种多功能开关，用于无标签的CRISPR/Cas12a传感器，具有自驱动放大

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-07-05 DOI: 10.1016/j.synbio.2025.07.002

Po Li , Xueying Lei , Xiaoying Niu , Wen Tian , Zhehuang Li , Songcheng Yu , Peng Zhang

引用次数: 0

Extracellular vesicles enhance the efficacy of ceftiofur against intracellular bacterial infections 细胞外囊泡增强头孢替福抗细胞内细菌感染的功效

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-07-03 DOI: 10.1016/j.synbio.2025.07.001

Pingping Yuan , Shijie Zhou , Qianqian Li , Lin Li , Shaoqi Qu

{"title":"Extracellular vesicles enhance the efficacy of ceftiofur against intracellular bacterial infections","authors":"Pingping Yuan , Shijie Zhou , Qianqian Li , Lin Li , Shaoqi Qu","doi":"10.1016/j.synbio.2025.07.001","DOIUrl":"10.1016/j.synbio.2025.07.001","url":null,"abstract":"<div><div>Bacterial infections pose a major threat to human health and economic stability. In particular, intracellular bacterial infections present significant clinical challenges due to antibiotic resistance and poor drug penetration. Therefore, there is an urgent need to develop novel therapeutic strategies to address the problem of intracellular bacterial infections. Extracellular bacterial vesicles become ideal delivery systems due to their natural targeting properties. Here, we developed a bacteria-derived extracellular vesicles (EVs)-based drug delivery platform to enhance the therapeutic efficacy of antibiotics against intracellular infections. EVs were successfully isolated and increased production from <em>S. aureus</em> by ultracentrifugation, then loaded with ceftiofur (CEF) via co-incubation. <em>In vitro</em> tests demonstrated the potent antibacterial activity of CEF, achieving complete growth inhibition within 24 h and a 4-log viability reduction in 4 h. Furthermore, confocal microscopy revealed efficient CEV internalization in IEC-6 cells, with 12-fold greater intracellular bacterial clearance than free CEF. <em>In vivo</em>, CEV-incorporated hydrogel (CEVH) significantly reduced both intra- and extracellular bacterial loads and accelerated wound healing. These findings demonstrate that bacterial EVs serve as a universal delivery platform to significantly enhance the efficacy of existing antibiotics against intracellular infections.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1200-1207"},"PeriodicalIF":4.4,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663487","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

Highly efficient genome editing in Bacillus subtilis via miniature DNA nucleases IscB 利用微型DNA核酸酶IscB对枯草芽孢杆菌进行高效基因组编辑

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-07-02 DOI: 10.1016/j.synbio.2025.06.012

Jie Gao, Hengyi Wang, Jingtao Sun, Hongjie Tang, Yuhan Yang, Qi Li

{"title":"Highly efficient genome editing in Bacillus subtilis via miniature DNA nucleases IscB","authors":"Jie Gao, Hengyi Wang, Jingtao Sun, Hongjie Tang, Yuhan Yang, Qi Li","doi":"10.1016/j.synbio.2025.06.012","DOIUrl":"10.1016/j.synbio.2025.06.012","url":null,"abstract":"<div><div>Existing CRISPR-based genome editing techniques for <em>Bacillus subtilis</em> (<em>B. subtilis</em>) are limited due to the large size of the <em>cas</em> gene. IscB, a recently reported DNA nuclease, is one-third the size of Cas9, making it a potential tool for genome editing; however, its application in <em>B. subtilis</em> remains unexplored. In this study, two IscB and enhanced IscB (enIscB)-based genome editing systems, named pBsuIscB and pBsuenIscB were established in <em>B. subtilis</em> SCK6, and their deletion efficiencies ranging from 13.3 % to 100 %. Compared to the pBsuIscB system, the pBsuenIscB system showed higher deletion efficiency, inducing the deletion of a large genomic fragment with a single ωRNA. Additionally, the pBsuenIscB system could integrate both single-copy and multi-copy <em>mCherry</em> genes in the <em>B. subtilis</em> SCK6 genome. Lastly, the pBsuenIscB system could efficiently conduct a second round of genome editing in <em>B. subtilis</em> SCK6. This study indicates that IscB can be used for genome editing in <em>B. subtilis</em>, enabling the efficient construction of engineered <em>B. subtilis</em> strains for large-scale biomolecule production.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1215-1223"},"PeriodicalIF":4.4,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680403","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

Rapid detection of genotoxicity employing an engineered high-sensitivity and tight SOS-response biosensor in Escherichia coli MG1655 利用工程化的高灵敏度、紧密sos反应生物传感器快速检测大肠杆菌MG1655的遗传毒性

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-27 DOI: 10.1016/j.synbio.2025.06.011

Xin Yuan , Wenliang Hao , Chong Zhang , Yizhi Ji , Yi Wang

{"title":"Rapid detection of genotoxicity employing an engineered high-sensitivity and tight SOS-response biosensor in Escherichia coli MG1655","authors":"Xin Yuan , Wenliang Hao , Chong Zhang , Yizhi Ji , Yi Wang","doi":"10.1016/j.synbio.2025.06.011","DOIUrl":"10.1016/j.synbio.2025.06.011","url":null,"abstract":"<div><div>Industrial wastewater and pesticide residues contain numerous genotoxic compounds that pose serious health risks by causing DNA damage and potentially triggering carcinogenesis. Conventional analytical methods such as chromatography and mass spectrometry are limited by high costs, technical complexity, and lengthy procedures, making them unsuitable for rapid, large-scale screening. To address this need, we developed a fluorescence-based SOS-responsive whole-cell biosensor (SRWCB) by integrating the P<sub><em>sulA</em></sub> promoter with superfolder GFP (sfGFP). Through directed evolution of the <em>lexA</em> binding motif in P<sub><em>sulA</em></sub>, we obtained an optimized variant (P55) with significantly enhanced sensitivity—being 8.5 times more sensitive than the commonly used P<sub><em>umuDC</em></sub> system—while maintaining rapid response kinetics. Further engineering via antisense transcription improved biosensor tightness without compromising induction efficiency. The final construct (SRWCB-55-J23119) successfully detected genotoxicants in industrial wastewater, demonstrating its practical applicability. This study presents a sensitive, rapid, and robust biosensor platform for high-throughput environmental genotoxicity monitoring.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"11 ","pages":"Pages 117-126"},"PeriodicalIF":4.4,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145096563","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

Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium stationis and its application in hypoxanthine biosynthesis 静止棒状杆菌CRISPR/Cas9基因组编辑工具箱的开发及其在次黄嘌呤生物合成中的应用

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-25 DOI: 10.1016/j.synbio.2025.06.010

Zhilin Ouyang , Xinyu Zhang , Xinyi Hou , Jiabei Huang , Ying Lin , Suiping Zheng

{"title":"Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium stationis and its application in hypoxanthine biosynthesis","authors":"Zhilin Ouyang , Xinyu Zhang , Xinyi Hou , Jiabei Huang , Ying Lin , Suiping Zheng","doi":"10.1016/j.synbio.2025.06.010","DOIUrl":"10.1016/j.synbio.2025.06.010","url":null,"abstract":"<div><div><em>Corynebacterium stationis</em>, a high-GC Gram-positive bacterium with significant industrial potential, has faced limitations due to the lack of efficient genetic tools. In this study, we developed a CRISPR/Cas9-based genome editing platform specifically tailored for <em>C. stationis</em>. First, electroporation efficiency was optimized to 1.81 ± 0.16 × 10<sup>5</sup> CFU (colony forming units)/μg plasmid DNA through medium selection, pulse parameter adjustments (2.5 kV, 2 pulses), and concentration optimization of cell wall-weakening agents (3.0 % glycine, 0.25 % isoniazid). Three functional shuttle vectors (p99E-pCG1, p19-Kan, p19-Spe) were constructed, enabling stable heterologous gene expression. By engineering a tightly regulated Cas9 expression system (P<em>lac</em> promoter with dual LacO∗ operators), we achieved high-efficiency genome editing, with deletion efficiencies of 81.2–98.6 % for 1.7–50 kb fragments and insertion efficiencies of 27.5–65.2 % for 1–5 kb fragments. CRISPR/Cas9-assisted ssDNA recombineering facilitated single/triple nucleotide changes with >90 % efficiency. Applying this toolbox, we engineered <em>C. stationis</em> for hypoxanthine biosynthesis by combining <em>purA</em> deletion with integration of heterologous feedback-resistant <em>prs</em><sup>D128A</sup> and endogenous <em>purF</em> deregulation (<em>purF</em><sup>K334Q</sup>), achieving a titer of 0.047 g/L. This study establishes a robust genetic platform for <em>C. stationis</em>, accelerating its industrial application in the production of biochemicals and biofuels.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1190-1199"},"PeriodicalIF":4.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144535761","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 Yarrowia lipolytica for high-level β-elemene production via combinatorial metabolic strategies 通过组合代谢策略使脂化耶氏菌高产β-榄香烯

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-25 DOI: 10.1016/j.synbio.2025.06.007

Mingyu Dai , Qingyi Cao , Shuanglong Jia, Jiang Chen, Hui-Ying Xu, Bang-Ce Ye, Wei-Bing Liu, Ying Zhou

{"title":"Engineering Yarrowia lipolytica for high-level β-elemene production via combinatorial metabolic strategies","authors":"Mingyu Dai , Qingyi Cao , Shuanglong Jia, Jiang Chen, Hui-Ying Xu, Bang-Ce Ye, Wei-Bing Liu, Ying Zhou","doi":"10.1016/j.synbio.2025.06.007","DOIUrl":"10.1016/j.synbio.2025.06.007","url":null,"abstract":"<div><div>β-Elemene, a pharmacologically active sesquiterpene derived from the traditional Chinese medicinal herb <em>Curcuma wenyujin</em>, exhibits broad-spectrum anti-tumor and anti-inflammatory activities. Currently, its commercial production relies heavily on plant extraction, a process associated with high costs and environmental burdens, limiting industrial scalability. To address these challenges, we developed a metabolically engineered <em>Yarrowia lipolytica</em> strain as an efficient microbial cell factory for de novo Germacrene A biosynthesis, the direct precursor of β-elemene. Through combinatorial optimization strategies—including (1) mevalonate (MVA) pathway enhancement, (2) copy number amplification of germacrene A synthase (GAS), (3) β-oxidation pathway reinforcement, and (4) introduction of the isopentenyl utilization pathway (IUP)—we significantly improved β-elemene production. The engineered strain achieved a titer of 3.08 ± 0.05 g/L in shake-flask cultures, with a yield of 51.27 ± 0.75 mg/g glucose, representing a 3.5-fold increase over the parental strain. Our work highlights the potential of <em>Y. lipolytica</em> as a sustainable and scalable platform for high-value sesquiterpene production, offering a viable alternative to plant-derived extraction.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1172-1179"},"PeriodicalIF":4.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144522717","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

Development of precise genome editing and multi-copy integration tools in Hansenula polymorpha DL-1 多态羊草DL-1精确基因组编辑和多拷贝整合工具的开发

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-24 DOI: 10.1016/j.synbio.2025.06.009

Xiaoyi Zou , Jiaqi Miao , Hongbiao Li , Yanshan Ke , Yan Chen , Weizhu Zeng , Jingwen Zhou

{"title":"Development of precise genome editing and multi-copy integration tools in Hansenula polymorpha DL-1","authors":"Xiaoyi Zou , Jiaqi Miao , Hongbiao Li , Yanshan Ke , Yan Chen , Weizhu Zeng , Jingwen Zhou","doi":"10.1016/j.synbio.2025.06.009","DOIUrl":"10.1016/j.synbio.2025.06.009","url":null,"abstract":"<div><div><em>Hansenula polymorpha</em> DL-1 is a thermotolerant yeast capable of utilizing multiple renewable carbon sources, making it a promising microbial cell factory for sustainable manufacturing. However, advanced metabolic engineering efforts have been constrained by its strong non-homologous end joining (NHEJ) mechanism and limited choice of suitable genetic tools. This study presents an optimized synthetic biology toolkit to address these limitations. A high-efficiency CRISPR-Cas9-based genome editing system was established, achieving an editing efficiency of 97.2 %. To further enhance homologous recombination (HR), the NHEJ pathway was partially suppressed by knocking out <em>KU80</em> and overexpressing HR-related genes from <em>Saccharomyces cerevisiae</em>. This increased HR rates to 88.9 %. In addition, 36 neutral sites were identified for stable single-copy gene integration without disrupting native gene expression cassettes. Finally, multi-copy integration tools were developed by targeting rDNA and Ty elements, leading to a ∼60-fold increase in β-carotene production compared with single-copy integrants. Furthermore, squalene titers were increased from 0.1 mg/L in the wild-type strain to 187.2 mg/L through iterative multi-copy integration. These advances significantly expand the genetic tractability of <em>H. polymorpha</em> DL-1, underscoring its potential as a versatile platform for efficient and sustainable production of value-added compounds.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1224-1233"},"PeriodicalIF":4.4,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144687427","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

From consultors to collaborators – An SOP for advancing ethics engagement in science 从顾问到合作者——促进科学伦理参与的标准操作程序

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-23 DOI: 10.1016/j.synbio.2025.06.006

Varsha Aravind Paleri, Kristien Hens

引用次数: 0