Synthetic and Systems Biotechnology最新文献_第4页

Systematic metabolic engineering of Yarrowia lipolytica for efficient production of phytohormone abscisic acid 利用脂肪分解酵母的系统代谢工程高效生产植物激素脱落酸

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-10-18 DOI: 10.1016/j.synbio.2024.10.004

Mei-Li Sun , Ziyun Zou , Lu Lin , Rodrigo Ledesma-Amaro , Kaifeng Wang , Xiao-Jun Ji

{"title":"Systematic metabolic engineering of Yarrowia lipolytica for efficient production of phytohormone abscisic acid","authors":"Mei-Li Sun , Ziyun Zou , Lu Lin , Rodrigo Ledesma-Amaro , Kaifeng Wang , Xiao-Jun Ji","doi":"10.1016/j.synbio.2024.10.004","DOIUrl":"10.1016/j.synbio.2024.10.004","url":null,"abstract":"<div><div>Abscisic acid (ABA) is an important phytohormone with diverse applications. It currently relies on the fermentation of <em>Botrytis cinerea</em>, which suffers from limited availability of genetic engineering tools. Here, <em>Yarrowia lipolytica</em> was engineered to enable <em>de novo</em> biosynthesis of ABA. To overcome the rate-limiting P450 enzymes, systematic engineering strategies were implemented. Firstly, the dissolved oxygen was increased to boost the activity of P450 enzymes. Secondly, the expansion of endoplasmic reticulum was implemented to improve the functional expression of P450 enzymes. Lastly, rate-limiting enzymes were assembled to facilitate substrate trafficking. Moreover, ABA production was further improved by strengthening the mevalonate pathway. Finally, the engineered strain produced 1221.45 mg/L of ABA in a 5-L bioreactor. The study provides effective approaches for alleviating rate-limiting P450 enzymes to enhance ABA production and achieve competitive industrial-level ABA production in <em>Y. lipolytica</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 165-173"},"PeriodicalIF":4.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553132","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

Enhancing substrate specificity of microbial transglutaminase for precise nanobody labeling 增强微生物转谷氨酰胺酶的底物特异性，实现精确的纳米抗体标记

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-10-16 DOI: 10.1016/j.synbio.2024.10.003

Xinglong Wang , Kangjie Xu , Haoran Fu , Qiming Chen , Beichen Zhao , Xinyi Zhao , Jingwen Zhou

{"title":"Enhancing substrate specificity of microbial transglutaminase for precise nanobody labeling","authors":"Xinglong Wang , Kangjie Xu , Haoran Fu , Qiming Chen , Beichen Zhao , Xinyi Zhao , Jingwen Zhou","doi":"10.1016/j.synbio.2024.10.003","DOIUrl":"10.1016/j.synbio.2024.10.003","url":null,"abstract":"<div><div><em>Streptomyces mobaraenesis</em> transglutaminase (smTG) can be used for site-specific labeling of proteins with chemical groups. Here, we explored the use of modified smTG for the biosynthesis of nanobody-fluorophore conjugates (NFC). smTG catalyzes the conjugation of acyl donors containing glutamine with lysine-containing acceptors, which can lead to non-specific cross-linking. To achieve precise site-specific labeling, we employed molecular docking and virtual mutagenesis to redesign the enzyme's substrate specificity towards the peptide GGGGQR, a non-preferred acyl donor for smTG. Starting with a thermostable and highly active smTG variant (TGm2), we identified that single mutations G250H and Y278E significantly enhanced activity against GGGGQR, increasing it by 41 % and 1.13-fold, respectively. Notably, the Y278E mutation dramatically shifted the enzyme's substrate preference, with the activity ratio against GGGGQR versus the standard substrate CBZ-Gln-Gly rising from 0.05 to 0.93. In case studies, we used nanobodies 1C12 and 7D12 as labeling targets, catalyzing their conjugation with a synthetic fluorophore via smTG variants. Nanobodies fused with GGGGQR were successfully site-specifically labeled by TGm2-Y278E, in contrast to non-specific labeling observed with other variants. These results suggest that engineering smTG for site-specific labeling is a promising approach for the biosynthesis of antibody-drug conjugates.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 185-193"},"PeriodicalIF":4.4,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553134","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

Mechanistic insights into the orthogonal functionality of an AHL-mediated quorum-sensing circuit in Yersinia pseudotuberculosis 对耶尔森氏菌假结核中 AHL 介导的法定量感应回路的正交功能的机理认识

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-10-14 DOI: 10.1016/j.synbio.2024.10.002

Boyu Luo , Shanshan Wu , Wei Liu , Dongdong Zhang , Ruicun Liu , Tuoyu Liu , Zhi Sun , Ziqun Wei , Mingyu Liu , Zhiyuan Shi , Niu Huang , Yue Teng

{"title":"Mechanistic insights into the orthogonal functionality of an AHL-mediated quorum-sensing circuit in Yersinia pseudotuberculosis","authors":"Boyu Luo , Shanshan Wu , Wei Liu , Dongdong Zhang , Ruicun Liu , Tuoyu Liu , Zhi Sun , Ziqun Wei , Mingyu Liu , Zhiyuan Shi , Niu Huang , Yue Teng","doi":"10.1016/j.synbio.2024.10.002","DOIUrl":"10.1016/j.synbio.2024.10.002","url":null,"abstract":"<div><div>YpsR, a pivotal regulatory protein in the quorum-sensing (QS) of <em>Yersinia pseudotuberculosis</em>(<em>Y. pstb</em>), is essential for molecular signaling, yet its molecular mechanisms remain poorly understood. Herein, this study systematically investigates the interactions between YpsR and acyl-homoserine lactones (AHLs), shedding light on the selective mechanism of YpsR to various AHL molecules. Using molecular docking and surface plasmon resonance (SPR) analysis, we confirmed YpsR's binding affinities, with the strongest observed for 3OC6-HSL, which notably inhibited <em>Y. pstb</em> growth. Additionally, we engineered a whole-cell biosensor based on YpsR-AHL interaction, which exhibited sensitivity to the signal molecule 3OC6-HSL produced by <em>Y. pstb</em>. Furthermore, key YpsR residues (S32, Y50, W54, D67) involved in AHL binding were identified and validated. Overall, this research elucidates the mechanisms of QS signal recognition in <em>Y. pstb</em>, providing valuable insights that support the development of diagnostic tools for detecting <em>Y. pstb</em> infections.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 174-184"},"PeriodicalIF":4.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553133","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

Revolutionizing biotechnology advances natural products discovery and industrial processing 生物技术的革命性进步推动了天然产品的发现和工业加工

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-10-04 DOI: 10.1016/j.synbio.2024.10.001

Yaojun Tong, Tilmann Weber

引用次数: 0

CRISPR/Cas12a-based genome editing for cyanophage of Anabeana sp. 基于 CRISPR/Cas12a 的蓝藻噬菌体基因组编辑技术

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-10-03 DOI: 10.1016/j.synbio.2024.09.011

Shengjian Yuan , Yanchen Li , Chunhua Kou , YiChen Sun , Yingfei Ma

{"title":"CRISPR/Cas12a-based genome editing for cyanophage of Anabeana sp.","authors":"Shengjian Yuan , Yanchen Li , Chunhua Kou , YiChen Sun , Yingfei Ma","doi":"10.1016/j.synbio.2024.09.011","DOIUrl":"10.1016/j.synbio.2024.09.011","url":null,"abstract":"<div><div>Efforts have been conducted on cyanobacterial genome editing, yet achieving genome editing in cyanophages remains challenging. Editing cyanophage genomes is crucial for understanding and manipulating their interactions with cyanobacterial hosts, offering potential solutions for controlling cyanobacterial blooms. In this study, we developed a streamlined CRISPR-Cas12a-based method for efficient cyanophage genome editing and then applied this method to the cyanophages A-1(L) and A-4(L) of <em>Anabeana</em> sp. PCC.7120. Multiple hypothetical genes were edited and knocked out from these two cyanophage genomes, generating viable mutants with varying capabilities to inhibit cyanobacterial growth. All these mutants displayed significant inhibitory effects on the host, indicating that these genes were non-essential for phage life cycle and the deletion led to little impairment of the cyanophages in infectious efficiency to their host. By iterative and simultaneous gene knockouts in cyanophage A-4(L), we achieved the minimal genome mutant with a 2400 bp reduction in genome size, representing a 5.75 % decrease compared to the wild type (WT). In conclusion, these cyanophage mutants can facilitate the identification of nonessential genes for cyanophages biology and the insertion of foreign genes for synthetic biology research. This advancement holds promise in addressing the widespread issue of water blooms and the associated environmental hazards.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 140-147"},"PeriodicalIF":4.4,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445510","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

Developing polycistronic expression tool in Yarrowia lipolytica 在脂溶性亚罗酵母中开发多聚组蛋白表达工具

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-09-28 DOI: 10.1016/j.synbio.2024.09.010

Donghan Li , Jianhui Liu , Lingxuan Sun , Jin Zhang , Jin Hou

引用次数: 0

Synthetic biotechnology for C1 bio-refinery 用于 C1 生物精炼厂的合成生物技术

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-09-23 DOI: 10.1016/j.synbio.2024.09.009

Yongjin Zhou (Chair Professor), Benjamin Woolston (Assistant Professor)

引用次数: 0

Transcriptome analysis reveals methanol metabolism variations for the growth damage caused by overexpression of chimeric transactivators in Pichia pastoris 转录组分析揭示了甲醇代谢变化对过量表达嵌合转录因子的 Pichia pastoris 生长造成的损害

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-09-23 DOI: 10.1016/j.synbio.2024.09.008

Qi Liu , Ziyu He , Menghao Cai

{"title":"Transcriptome analysis reveals methanol metabolism variations for the growth damage caused by overexpression of chimeric transactivators in Pichia pastoris","authors":"Qi Liu , Ziyu He , Menghao Cai","doi":"10.1016/j.synbio.2024.09.008","DOIUrl":"10.1016/j.synbio.2024.09.008","url":null,"abstract":"<div><div>Methanol is a promising substrate for sustainable biomanufacturing, and <em>Pichia pastoris</em> has become a commonly used yeast for methanol utilization due to its powerful methanol metabolic pathways and methanol inducible promoter. Previous reconstruction of gene circuits highly improved transcriptional activity, but excessive expression of chimeric transactivator damaged cell growth on methanol. Here we employed transcriptome analysis to investigate the effects of chimeric transactivator overexpression on cellular metabolism and regulatory networks. The results showed that strong expression of chimeric transactivator unexpectedly downregulated methanol metabolism, especially the <em>alcohol oxidase 1</em> (<em>AOX1</em>), but without remarkable changes in expression of transcriptional factors. Meanwhile, the synthesis of peroxisomes also varied with chimeric transactivator expression. In addition, the enrichment analysis of differentially expressed genes revealed their impact on cellular metabolism. The gene expression patterns caused by different expression levels of chimeric transactivators have also been clarified. This work provides useful information to understand the transcriptional regulation of the <em>AOX1</em> promoter and methanol signaling. It revealed the importance of balancing transcription factor expression for the host improvement.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 133-139"},"PeriodicalIF":4.4,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445509","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

Efficient biosynthesis of β-caryophyllene in Saccharomyces cerevisiae by β-caryophyllene synthase from Artemisia argyi 艾蒿中的β-石竹烯合成酶在酿酒酵母中高效生物合成β-石竹烯

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-09-22 DOI: 10.1016/j.synbio.2024.09.005

Zhengping Li , Yuhong Gan , Changyu Gou , Qiongyu Ye , Yang Wu , Yuhong Wu , Tingxing Yang , Baolian Fan , Aijia Ji , Qi Shen , Lixin Duan

{"title":"Efficient biosynthesis of β-caryophyllene in Saccharomyces cerevisiae by β-caryophyllene synthase from Artemisia argyi","authors":"Zhengping Li , Yuhong Gan , Changyu Gou , Qiongyu Ye , Yang Wu , Yuhong Wu , Tingxing Yang , Baolian Fan , Aijia Ji , Qi Shen , Lixin Duan","doi":"10.1016/j.synbio.2024.09.005","DOIUrl":"10.1016/j.synbio.2024.09.005","url":null,"abstract":"<div><div><em>Artemisia argyi</em> H. Lév. & Vaniot is an important traditional Chinese medicinal plant known for its volatile oils, which are the main active components of <em>A. argyi</em>, including monoterpenes, sesquiterpenes and their derivatives. Despite its medicinal significance, the biosynthesis of sesquiterpenoids in <em>A. argyi</em> remains underexplored. In this study, we identified four <em>β</em>-caryophyllene synthases from <em>A. argyi.</em> A high-yield <em>β</em>-caryophyllene engineered <em>Saccharomyces cerevisiae</em> cell factory has been built in this study. By fusing <em>ERG20</em> and <em>AarTPS88</em> with a flexible linker (GGGS)<sub>2</sub> and enhancing metabolic flux in the MVA pathway (<em>HIF-1</em>, <em>tHMGR</em>, and <em>UPC2-1</em>), we achieved a titer of <em>β</em>-caryophyllene reached 15.6 g/L by fed-batch fermentation in a 5 L bioreactor. To our knowledge, this represents the highest reported titer of <em>β</em>-caryophyllene in yeast to date. This study provides a valuable tool for the industrial-scale production of <em>β</em>-caryophyllene.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 158-164"},"PeriodicalIF":4.4,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142533920","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 a green Komagataella phaffii cell factory for sustainable production of plant-derived sesquiterpene (–)-α-bisabolol 开发绿色 Komagataella phaffii 细胞工厂，以可持续方式生产植物源倍半萜 (-)-α-bisabolol

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2024-09-17 DOI: 10.1016/j.synbio.2024.09.006

Jintao Cheng , Zhongji Pu , Jiali Chen , Dingfeng Chen , Baoxian Li , Zhengshun Wen , Yuanxiang Jin , Yanlai Yao , Kan Shao , Xiaosong Gu , Guiling Yang

{"title":"Development of a green Komagataella phaffii cell factory for sustainable production of plant-derived sesquiterpene (–)-α-bisabolol","authors":"Jintao Cheng , Zhongji Pu , Jiali Chen , Dingfeng Chen , Baoxian Li , Zhengshun Wen , Yuanxiang Jin , Yanlai Yao , Kan Shao , Xiaosong Gu , Guiling Yang","doi":"10.1016/j.synbio.2024.09.006","DOIUrl":"10.1016/j.synbio.2024.09.006","url":null,"abstract":"<div><div>(–)-α-Bisabolol is a plant-derived sesquiterpene derived from <em>Eremanthus erythropappus,</em> which can be used as a raw material in cosmetics and has anti-inflammatory function. In this study, we designed six mutation sites of the (–)-α-bisabolol synthase BOS using the plmDCA algorithm. Among these, the F324Y mutation demonstrated exceptional performance, increasing the product yield by 73 %. We constructed a <em>de novo</em> (–)-α-bisabolol biosynthesis pathways through systematic synthetic biology strategies, including the enzyme design of BOS, selection of different linkers in fusion expression, and optimization of the mevalonate pathway, weakening the branching metabolic flow and multi-copy strategies, the yield of (–)-α-bisabolol was significantly increased, which was nearly 35-fold higher than that of the original strain (2.03 mg/L). The engineered strain was capable of producing 69.7 mg/L in shake flasks. To the best of our knowledge, this is the first report on the biosynthesis of (–)-α-bisabolol in <em>Komagataella phaffii</em>, implying this is a robust cell factory for sustainable production of other terpenoids.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 1","pages":"Pages 120-126"},"PeriodicalIF":4.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445489","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