Synthetic and Systems Biotechnology最新文献_第5页

Combinatorial metabolic engineering of Escherichia coli for de novo production of structurally defined and homogeneous Amino oligosaccharides 利用大肠杆菌的组合代谢工程从头生产结构明确的同质氨基寡糖

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-21 DOI: 10.1016/j.synbio.2024.05.011

Jinqi Shi , Chen Deng , Chunyue Zhang , Shu Quan , Liqiang Fan , Liming Zhao

{"title":"Combinatorial metabolic engineering of Escherichia coli for de novo production of structurally defined and homogeneous Amino oligosaccharides","authors":"Jinqi Shi , Chen Deng , Chunyue Zhang , Shu Quan , Liqiang Fan , Liming Zhao","doi":"10.1016/j.synbio.2024.05.011","DOIUrl":"10.1016/j.synbio.2024.05.011","url":null,"abstract":"<div><p>Amino oligosaccharides (AOs) possess various biological activities and are valuable in the pharmaceutical, food industries, and agriculture. However, the industrial manufacturing of AOs has not been realized yet, despite reports on physical, chemical, and biological approaches. In this study, the <em>de novo</em> production of chitin oligosaccharides (CHOS), a type of structurally defined AOs, was achieved in <em>Escherichia coli</em> through combinatorial pathway engineering. The most suitable glycosyltransferase for CHOS production was found to be NodCL from <em>Mesorhizobium Loti</em>. Then, by knocking out the <em>nagB</em> gene to block the flow of N-acetyl-<span>d</span>-glucosamine (NAG) to the glycolytic pathway in <em>E. coli</em> and adjusting the copy number of NodCL-coding gene, the CHOS yield was increased by 6.56 times. Subsequently, by introducing of UDP-N-acetylglucosamine (UDP-GlcNAc) <em>salvage</em> pathway for and optimizing fermentation conditions, the yield of CHOS reached 207.1 and 468.6 mg/L in shake-flask cultivation and a 5-L fed-batch bioreactor, respectively. Meanwhile, the concentration of UDP-GlcNAc was 91.0 mg/L, the highest level reported in <em>E. coli</em> so far. This study demonstrated, for the first time, the production of CHOS with distinct structures in plasmid-free <em>E. coli</em>, laying the groundwork for the biosynthesis of CHOS and providing a starting point for further engineering and commercial production.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000863/pdfft?md5=5c0ca8265585c2434e8e346f77cfebf0&pid=1-s2.0-S2405805X24000863-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141136653","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

Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches 利用反向疫苗学和免疫信息学方法开发针对艰难梭菌的多表位 mRNA 疫苗

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-18 DOI: 10.1016/j.synbio.2024.05.008

Caixia Tan , Yuanyuan xiao , Ting Liu , Siyao Chen , Juan Zhou , Sisi Zhang , Yiran Hu , Anhua Wu , Chunhui Li

{"title":"Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches","authors":"Caixia Tan , Yuanyuan xiao , Ting Liu , Siyao Chen , Juan Zhou , Sisi Zhang , Yiran Hu , Anhua Wu , Chunhui Li","doi":"10.1016/j.synbio.2024.05.008","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.05.008","url":null,"abstract":"<div><p><em>Clostridioides difficile</em> (<em>C. difficile</em>), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for <em>Clostridioides difficile</em> infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against <em>C. difficile</em> is of paramount importance. In our study, the complete proteome sequences of 118 strains of <em>C. difficile</em> were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000838/pdfft?md5=c0004b11a30ad7b49ee9863aa380bea4&pid=1-s2.0-S2405805X24000838-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141073091","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

A generative benchmark for evaluating the performance of fluorescent cell image segmentation 评估荧光细胞图像分割性能的生成基准

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-17 DOI: 10.1016/j.synbio.2024.05.005

Jun Tang , Wei Du , Zhanpeng Shu , Zhixing Cao

{"title":"A generative benchmark for evaluating the performance of fluorescent cell image segmentation","authors":"Jun Tang , Wei Du , Zhanpeng Shu , Zhixing Cao","doi":"10.1016/j.synbio.2024.05.005","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.05.005","url":null,"abstract":"<div><p>Fluorescent cell imaging technology is fundamental in life science research, offering a rich source of image data crucial for understanding cell spatial positioning, differentiation, and decision-making mechanisms. As the volume of this data expands, precise image analysis becomes increasingly critical. Cell segmentation, a key analysis step, significantly influences quantitative analysis outcomes. However, selecting the most effective segmentation method is challenging, hindered by existing evaluation methods' inaccuracies, lack of graded evaluation, and narrow assessment scope. Addressing this, we developed a novel framework with two modules: StyleGAN2-based contour generation and Pix2PixHD-based image rendering, producing diverse, graded-density cell images. Using this dataset, we evaluated three leading cell segmentation methods: DeepCell, CellProfiler, and CellPose. Our comprehensive comparison revealed CellProfiler's superior accuracy in segmenting cytoplasm and nuclei. Our framework diversifies cell image data generation and systematically addresses evaluation challenges in cell segmentation technologies, establishing a solid foundation for advancing research and applications in cell image analysis.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000802/pdfft?md5=13815bcd26120681d6104aa2879c4302&pid=1-s2.0-S2405805X24000802-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140950918","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

A highly efficient method for genomic deletion across diverse lengths in thermophilic Parageobacillus thermoglucosidasius 嗜热副乳杆菌不同长度基因组删除的高效方法

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-17 DOI: 10.1016/j.synbio.2024.05.009

Zhiheng Yang , Bixiao Li , Ruihong Bu , Zhengduo Wang , Zhenguo Xin , Zilong Li , Lixin Zhang , Weishan Wang

{"title":"A highly efficient method for genomic deletion across diverse lengths in thermophilic Parageobacillus thermoglucosidasius","authors":"Zhiheng Yang , Bixiao Li , Ruihong Bu , Zhengduo Wang , Zhenguo Xin , Zilong Li , Lixin Zhang , Weishan Wang","doi":"10.1016/j.synbio.2024.05.009","DOIUrl":"10.1016/j.synbio.2024.05.009","url":null,"abstract":"<div><p><em>Parageobacillus thermoglucosidasius</em> is emerging as a highly promising thermophilic organism for metabolic engineering. The utilization of CRISPR-Cas technologies has facilitated programmable genetic manipulation in <em>P. thermoglucosidasius</em>. However, the absence of thermostable NHEJ enzymes limited the capability of the endogenous type I CRISPR-Cas system to generate a variety of extensive genomic deletions. Here, two thermophilic NHEJ enzymes were identified and combined with the endogenous type I CRISPR-Cas system to develop a genetic manipulation tool that can achieve long-range genomic deletion across various lengths. By optimizing this tool—through adjusting the expression level of NHEJ enzymes and leveraging our discovery of a negative correlation between GC content of the guide RNA (gRNA) and deletion efficacy—we streamlined a comprehensive gRNA selection manual for whole-genome editing, achieving a 100 % success rate in randomly selecting gRNAs. Notably, using just one gRNA, we achieved genomic deletions spanning diverse length, exceeding 200 kilobases. This tool will facilitate the genomic manipulation of <em>P. thermoglucosidasius</em> for both fundamental research and applied engineering studies, further unlocking its potential as a thermophilic cell factory.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X2400084X/pdfft?md5=c0ba3cfd0579149a88026a1bb7d806af&pid=1-s2.0-S2405805X2400084X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141051563","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

Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes in Escherichia coli 自动表征和分析大肠杆菌中调控序列与代谢基因之间的表达兼容性

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-17 DOI: 10.1016/j.synbio.2024.05.010

Xiao Wen , Jiawei Lin , Chunhe Yang , Ying Li , Haijiao Cheng , Ye Liu , Yue Zhang , Hongwu Ma , Yufeng Mao , Xiaoping Liao , Meng Wang

{"title":"Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes in Escherichia coli","authors":"Xiao Wen , Jiawei Lin , Chunhe Yang , Ying Li , Haijiao Cheng , Ye Liu , Yue Zhang , Hongwu Ma , Yufeng Mao , Xiaoping Liao , Meng Wang","doi":"10.1016/j.synbio.2024.05.010","DOIUrl":"10.1016/j.synbio.2024.05.010","url":null,"abstract":"<div><p>Utilizing standardized artificial regulatory sequences to fine-tuning the expression of multiple metabolic pathways/genes is a key strategy in the creation of efficient microbial cell factories. However, when regulatory sequence expression strengths are characterized using only a few reporter genes, they may not be applicable across diverse genes. This introduces great uncertainty into the precise regulation of multiple genes at multiple expression levels. To address this, our study adopted a fluorescent protein fusion strategy for a more accurate assessment of target protein expression levels. We combined 41 commonly-used metabolic genes with 15 regulatory sequences, yielding an expression dataset encompassing 520 unique combinations. This dataset highlighted substantial variation in protein expression level under identical regulatory sequences, with relative expression levels ranging from 2.8 to 176-fold. It also demonstrated that improving the strength of regulatory sequences does not necessarily lead to significant improvements in the expression levels of target proteins. Utilizing this dataset, we have developed various machine learning models and discovered that the integration of promoter regions, ribosome binding sites, and coding sequences significantly improves the accuracy of predicting protein expression levels, with a Spearman correlation coefficient of 0.72, where the promoter sequence exerts a predominant influence. Our study aims not only to provide a detailed guide for fine-tuning gene expression in the metabolic engineering of <em>Escherichia coli</em> but also to deepen our understanding of the compatibility issues between regulatory sequences and target genes.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000851/pdfft?md5=f535dd3094336720674eaf7d8d922be9&pid=1-s2.0-S2405805X24000851-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141042170","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

Laccase is a multitasking protein for synthetic gene circuits in the yeast Saccharomyces cerevisiae 漆酶是酵母中合成基因回路的多任务蛋白质

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-14 DOI: 10.1016/j.synbio.2024.05.007

Lifang Yu , Michael Dare Asemoloye , Mario Andrea Marchisio

{"title":"Laccase is a multitasking protein for synthetic gene circuits in the yeast Saccharomyces cerevisiae","authors":"Lifang Yu , Michael Dare Asemoloye , Mario Andrea Marchisio","doi":"10.1016/j.synbio.2024.05.007","DOIUrl":"10.1016/j.synbio.2024.05.007","url":null,"abstract":"<div><p>Laccase is a multicopper oxidase enzyme that oxidizes a variety of substrates, including polyphenols and polycyclic aromatic hydrocarbons (PAHs). It catalyzes the four-electron reduction of molecular oxygen that results in the production of water as a by-product. Thus, laccase can play an important role in environmental care. Previously, we have successfully expressed <em>Trametes trogii</em> laccase (TtLcc1) in the yeast <em>Saccharomyces cerevisiae</em>. In this work, we have expressed in yeast another laccase, LacA from <em>Trametes</em> sp. AH28-2, and tested its function on PAHs. Yeast cells engineered to produce the two laccases performed efficient PAH degradation. Both TtLcc1 and LacA led to the construction of spatiotemporal fluorescence-pulse generators when combined with a benzoate/salicylate yeast biosensor in a two-population system. Moreover, laccases returned a visual output signal in yeast synthetic circuits—upon reacting with ABTS (2,2′-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid)). Thus, in <em>S. cerevisiae</em>, laccases are a powerful alternative to fluorescent reporter proteins.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000826/pdfft?md5=94b4a3b771a037d03930700fdbebb1a0&pid=1-s2.0-S2405805X24000826-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141042589","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

Biochemical synthesis of taxanes from mevalonate 从甲羟戊酸中生化合成紫杉类化合物

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-13 DOI: 10.1016/j.synbio.2024.05.002

Jing Li , Xiaonan Liu , Xiaoxi Zhu , Jiayu Liu , Lei Zhang , Nida Ahmed , Jian Qi , Bihuan Chen , Daliang Tang , Jinsheng Yu , Zhijin Fan , Huifeng Jiang

{"title":"Biochemical synthesis of taxanes from mevalonate","authors":"Jing Li , Xiaonan Liu , Xiaoxi Zhu , Jiayu Liu , Lei Zhang , Nida Ahmed , Jian Qi , Bihuan Chen , Daliang Tang , Jinsheng Yu , Zhijin Fan , Huifeng Jiang","doi":"10.1016/j.synbio.2024.05.002","DOIUrl":"10.1016/j.synbio.2024.05.002","url":null,"abstract":"<div><p>Taxanes are kinds of diterpenoids with important bioactivities, such as paclitaxel (taxol®) is an excellent natural broad-spectrum anticancer drug. Attempts to biosynthesize taxanes have made with limited success, mainly due to the bottleneck of the low efficiency catalytic elements. In this study, we developed an artificial synthetic system to produce taxanes from mevalonate (MVA) by coupling biological and chemical methods, which comprises <em>in vitro</em> multi-enzyme catalytic module, chemical catalytic module and yeast cell catalytic module. Through optimizing <em>in vitro</em> multienzyme catalytic system, the yield of taxadiene was increased to 946.7 mg/L from MVA within 8 h and the productivity was 14.2-fold higher than microbial fermentation. By incorporating palladium catalysis, the conversion rate of Taxa-4(20),11(12)-dien-5α-yl acetate (T5α-AC) reached 48 %, effectively addressing the product promiscuity and the low yield rate of T5αOH. Finally, we optimized the expression of T10βOH in yeast resulting in the biosynthesis of Taxa-4(20),11(12)-dien-5α-acetoxy-10β-ol(T5α-AC-10β-ol) at a production of 15.8 mg/L, which displayed more than 2000-fold higher than that produced by co-culture fermentation strategy. These technologies offered a promising new approach for efficient synthesis of taxanes.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X2400070X/pdfft?md5=9bc12b054aaa058a77e0a0cdc2b83996&pid=1-s2.0-S2405805X2400070X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141037752","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

New N-acylated aminoalkanoic acids from tea roots derived biocontrol agent Clonostachys rosea 15020 从茶叶根部提取的新型 N-酰化氨基烷酸生物控制剂 Clonostachys rosea 15020

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-11 DOI: 10.1016/j.synbio.2024.05.006

Jiaming Yu , Yue Zhang , Li Zhang , Jie Shi , Kun Wang , Weize Yuan , Zexu Lin , Shangqian Ning , Bohao Wang , Xinye Wang , Yuyang Qiu , Tom Hsiang , Lixin Zhang , Xueting Liu , Guoliang Zhu

{"title":"New N-acylated aminoalkanoic acids from tea roots derived biocontrol agent Clonostachys rosea 15020","authors":"Jiaming Yu , Yue Zhang , Li Zhang , Jie Shi , Kun Wang , Weize Yuan , Zexu Lin , Shangqian Ning , Bohao Wang , Xinye Wang , Yuyang Qiu , Tom Hsiang , Lixin Zhang , Xueting Liu , Guoliang Zhu","doi":"10.1016/j.synbio.2024.05.006","DOIUrl":"10.1016/j.synbio.2024.05.006","url":null,"abstract":"<div><p>Four new <em>N</em>-acylated aminoalkanoic acids, namely clonoroseins E−H (<strong>1</strong>−<strong>4</strong>), together with three previously identified analogs, clonoroseins A, B, and D (<strong>5</strong>−<strong>7</strong>), were identified from the endophytic fungus <em>Clonostachys rosea</em> strain 15020 (CR15020), using Feature-based Molecular Networking (FBMN). The elucidation of their chemical structures, including their absolute configurations, was achieved through spectroscopic analysis combined with quantum chemical calculations. Bioinformatics analyses suggested that an iterative type I HR-PKS (CrsE) generates the polyketide side chain of these clonoroseins. Furthermore, a downstream adenylate-forming enzyme of the PKS (CrsD) was suspected to function as an amide synthetase. CrsD potentially facilitates the transformation of the polyketide moiety into an acyl-AMP intermediate, followed by nucleophilic substitution with either β-alanine or γ-aminobutyric acid to produce amide derivatives. These findings significantly expand our understanding of PKS-related products originating from <em>C. rosea</em> and also underscore the powerful application of FBMN analytical methods in characterization of new compounds.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000814/pdfft?md5=01cef55bed96e72c42a2b3604900de88&pid=1-s2.0-S2405805X24000814-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141027199","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

Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica 油脂酵母亚罗酵母基因表达和操作的进展与前景

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-10 DOI: 10.1016/j.synbio.2024.05.003

Mengchen Hu, Jianyue Ge, Yaru Jiang, Xiaoman Sun, Dongshen Guo, Yang Gu

{"title":"Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica","authors":"Mengchen Hu, Jianyue Ge, Yaru Jiang, Xiaoman Sun, Dongshen Guo, Yang Gu","doi":"10.1016/j.synbio.2024.05.003","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.05.003","url":null,"abstract":"<div><p>The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, <em>Yarrowia lipolytica</em>, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to <em>Y. lipolytica</em>, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a <em>Y. lipolytica</em> microbial factory.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000711/pdfft?md5=c495d2ca89fba481587179d504cd2b75&pid=1-s2.0-S2405805X24000711-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140918634","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

The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa LysR家族转录调控因子ORF-L16调控刺五加的生物合成

IF 4.8 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-05-10 DOI: 10.1016/j.synbio.2024.05.001

Xin Mu , Ru Lei , Shuqing Yan , Zixin Deng , Ran Liu , Tiangang Liu

{"title":"The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa","authors":"Xin Mu , Ru Lei , Shuqing Yan , Zixin Deng , Ran Liu , Tiangang Liu","doi":"10.1016/j.synbio.2024.05.001","DOIUrl":"https://doi.org/10.1016/j.synbio.2024.05.001","url":null,"abstract":"<div><p>Spinosad, a potent broad-spectrum bioinsecticide produced by <em>Saccharopolyspora spinosa</em>, has significant market potential. Despite its effectiveness, the regulatory mechanisms of spinosad biosynthesis remain unclear. Our investigation identified the crucial role of the LysR family transcriptional regulator ORF-L16, located upstream of spinosad biosynthetic genes, in spinosad biosynthesis. Through reverse transcription PCR (RT-PCR) and 5′-rapid amplification of cDNA ends (5′-Race), we unveiled that the spinosad biosynthetic gene cluster (BGC) contains six transcription units and seven promoters. Electrophoretic mobility shift assays (EMSAs) demonstrated that ORF-L16 bound to seven promoters within the spinosad BGC, indicating its involvement in regulating spinosad biosynthesis. Notably, deletion of <em>ORF-L16</em> led to a drastic reduction in spinosad production from 1818.73 mg/L to 1.69 mg/L, accompanied by decreased transcription levels of spinosad biosynthetic genes, confirming its positive regulatory function. Additionally, isothermal titration calorimetry (ITC) and EMSA confirmed that spinosyn A, the main product of the spinosad BGC, served as an effector of ORF-L16. Specifically, it decreased the binding affinity between ORF-L16 and spinosad BGC promoters, thus exerting negative feedback regulation on spinosad biosynthesis. This research enhances our comprehension of spinosad biosynthesis regulation and lays the groundwork for future investigations on transcriptional regulators in <em>S. spinosa</em>.</p></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2405805X24000693/pdfft?md5=7b0b5533316d925759dda110575da5c6&pid=1-s2.0-S2405805X24000693-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140914436","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