Synthetic and Systems Biotechnology最新文献_第2页

PEX3 gene knockout influences recombinant xylanase expression by Komagataella phaffii PEX3 基因敲除影响 Komagataella phaffii 重组木聚糖酶的表达

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-28 DOI: 10.1016/j.synbio.2025.03.010

Ziwei Zhou, Wenjie Cong, Mingxuan Wang, Hualan Zhou, Jianguo Zhang

{"title":"PEX3 gene knockout influences recombinant xylanase expression by Komagataella phaffii","authors":"Ziwei Zhou, Wenjie Cong, Mingxuan Wang, Hualan Zhou, Jianguo Zhang","doi":"10.1016/j.synbio.2025.03.010","DOIUrl":"10.1016/j.synbio.2025.03.010","url":null,"abstract":"<div><div><em>Komagataella phaffii</em> is a methylotrophic yeast harboring a tightly regulated alcohol oxidase promoter (<em>P</em><sub><em>AOX1</em></sub>), which is now widely used for recombinant protein production. During <em>P</em><sub><em>AOX1</em></sub> expression phase by methanol induction, a methanol metabolism organelle peroxisome enlarged and occupied 80 % of <em>K. phaffii</em> cell through peroxins functions of matrix protein import and organelle division. Using a <em>K. phaffii</em> expressing xylanase in this study, each of all 23 <em>PEX</em> genes of <em>K. phaffii</em>, encoding peroxin, was knockout to influence the peroxisome size, leading to changes of <em>K. phaffii</em> physiological status and recombinant xylanase expression. It was observed that <em>PEX3</em> knockout reduced peroxisome size by 54.3 %, increased xylanase expression by 29 %, decreased apoptosis ratio by 70.6 %. Transcriptome analysis revealed that <em>PEX3</em> gene knockout decreased 18 other <em>PEX</em> genes of all three steps of peroxisome propagation, biogenesis, matrix protein import, and peroxisome fission. <em>PEX3</em> gene knockout influenced expression of ribosomal subunit-related and protein transportation significantly based on gene function annotation and enrichment analysis. Additionally, Therefore, <em>PEX3</em> gene knockout promoted xylanase folding correctly via Sec63 complex, and PDI1 significantly. In a summary, <em>PEX3</em> gene knockout provided a novel strategy to enhance recombinant xylanase by <em>K. phaffii</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 764-773"},"PeriodicalIF":4.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143783415","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

iCASRED, a scarless DNA editing tool in E. coli for high-efficiency engineering of natural product biosynthetic gene clusters iCASRED，大肠杆菌无疤痕DNA编辑工具，用于天然产物生物合成基因簇的高效工程

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-20 DOI: 10.1016/j.synbio.2025.03.008

Guosong Zheng , Jiafeng Xu , Hewei Liu , Huimin Hua , Andrei A. Zimin , Wenfang Wang , Yinhua Lu

{"title":"iCASRED, a scarless DNA editing tool in E. coli for high-efficiency engineering of natural product biosynthetic gene clusters","authors":"Guosong Zheng , Jiafeng Xu , Hewei Liu , Huimin Hua , Andrei A. Zimin , Wenfang Wang , Yinhua Lu","doi":"10.1016/j.synbio.2025.03.008","DOIUrl":"10.1016/j.synbio.2025.03.008","url":null,"abstract":"<div><div>Efficient gene cluster editing tools are one of the key techniques for discovering novel compounds encoded by silent natural product (NP) biosynthetic gene clusters (BGCs) in microbial genomes. Currently, <em>in vivo</em> BGC editing tools developed in <em>E</em>. <em>coli</em> is the most widely used, but they often introduces DNA scars into gene clusters, which may affect the function of target NP BGCs. Herein, a genome-<u>i</u>ntegrated <u>Cas</u>9/λ<u>Red</u> system-based <em>in vivo</em> scarless gene cluster editing tool (iCASRED) was established in <em>E. coli</em> BL23, which was constructed on the basis of BL21/DE3 with <em>recA</em> deletion and simultaneous integration of an inducible sgRNA targeting the editing plasmid (an all-in-one plasmid with the BGC-targeting sgRNAs and repair templates). iCASRED achieved scarless editing of single targets in three tested gene clusters (44.2, 72.0, and 76.2 kb) cloned in either a single-copy BAC plasmid or a high-copy plasmid pCAP01 with the efficiencies of 28.8 % ± 3.9 %–100 % ± 0 %. Furthermore, this tool could enable convenient, high-efficiency iterative editing. Finally, we achieved 24.4 % ± 3.8 % efficiency for simultaneous double-target editing by replacing Cas9 by nCas9 (Cas9<sup>D10A</sup>). Collectively, iCASRED provides a simple, convenient, and cost-effective approach for engineering gene clusters, which may facilitate the discovery of novel NPs and strain improvements for high-yield of target compounds.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 751-763"},"PeriodicalIF":4.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776814","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

Enhanced chlorogenic acid production from glucose via systematic metabolic engineering of Saccharomyces cerevisiae 通过酿酒酵母系统代谢工程提高葡萄糖产绿原酸

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-20 DOI: 10.1016/j.synbio.2025.03.004

Shuai Tu, Junjie Wang, Pengming Yang, Yan He, Zhixing Gong, Weihong Zhong

{"title":"Enhanced chlorogenic acid production from glucose via systematic metabolic engineering of Saccharomyces cerevisiae","authors":"Shuai Tu, Junjie Wang, Pengming Yang, Yan He, Zhixing Gong, Weihong Zhong","doi":"10.1016/j.synbio.2025.03.004","DOIUrl":"10.1016/j.synbio.2025.03.004","url":null,"abstract":"<div><div>Chlorogenic acid (CGA) is a valuable phenolic acid with various pharmaceutical functions. In our previous study, <em>de novo</em> synthesis of CGA in <em>Saccharomyces cerevisiae</em> was achieved. However, its yield required improvement before large scale production. In this study, systematic metabolic engineering strategy was used to reconstruct chassis cell <em>S</em>. <em>cerevisiae</em> YC0707 to enhance its CGA yield from glucose. To balance the supply of phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P), <em>ZWF1</em> (encoding glucose-6-phosphate dehydrogenase) and <em>GND1</em> (encoding 6-phosphogluconate dehydrogenase) were overexpressed by strong promoter <em>P</em><sub><em>TEF1</em></sub> swapping, thereby strengthening the pentose phosphate pathway. The mutant of phosphofructokinase (<em>PFK2</em><sup><em>S718D</em></sup>) was further introduced to weaken the glycolytic pathway. Then, the <em>p</em>-coumaric acid synthesis capacity was enhanced by employing tyrosine ammonia lyase from <em>Rhodotorula glutinis</em> (RgTAL), ΔHAM1, and ΔYJL028W. Fusion expression of AtC4H (cinnamate-4-hydroxylase) and At4CL1 (4-coumarate CoA ligase 1), together with CsHQT (hydroxycinnamoyl CoA quinate transferase) and AtC3′H (<em>p</em>-coumaroyl shikimate 3-hydroxylase), improved biosynthetic flux to CGA. Subsequently, the microenvironment of P450 enzymes was improved by overexpressing <em>INO2</em> (a transcription factor for lipid biosynthesis) and removal of heme oxygenase gene <em>HMX1</em>. Furthermore, screening potential transporters to facilitate CGA accumulation. Finally, we optimized the fermentation conditions. Using these strategies, CGA titers increased from 234.8 mg/L to 837.2 mg/L in shake flasks and reached 1.62 g/L in a 5-L bioreactor, representing the highest report in <em>S. cerevisiae</em> and providing new insights for CGA production.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 707-718"},"PeriodicalIF":4.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776810","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

Identification of two new flavone 4′-O-methyltransferases and their application in de novo biosynthesis of (2S)-hesperetin in Yarrowia lipolytica 两种新的黄酮4′- o -甲基转移酶的鉴定及其在脂性耶氏菌（Yarrowia polylitica） (2S)-橙皮素的生物合成中的应用

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-20 DOI: 10.1016/j.synbio.2025.03.003

Yiyun Wang , Ruiqiu Huang , Song Gao , Mingyu Yue , Xuan Zhang , Weizhu Zeng , Bin Tang , Jingwen Zhou , Dongliang Huang , Sha Xu

{"title":"Identification of two new flavone 4′-O-methyltransferases and their application in de novo biosynthesis of (2S)-hesperetin in Yarrowia lipolytica","authors":"Yiyun Wang , Ruiqiu Huang , Song Gao , Mingyu Yue , Xuan Zhang , Weizhu Zeng , Bin Tang , Jingwen Zhou , Dongliang Huang , Sha Xu","doi":"10.1016/j.synbio.2025.03.003","DOIUrl":"10.1016/j.synbio.2025.03.003","url":null,"abstract":"<div><div>Methyltransferases are pivotal enzymes in the biosynthesis of methylated flavonoids, including (2<em>S</em>)-hesperetin. However, existing flavonoid 4′-<em>O</em>-methyltransferase (F4′OMT) enzymes typically exhibit low substrate specificity and catalytic efficiency, which hinders microbial synthesis. To overcome this limitation, this study screened and identified two novel F4′OMTs, <em>Crc</em>OMT-2 and <em>Cgt</em>OMT-3, from Chinese citrus varieties <em>Citrus reticulata</em> ‘Chachiensis’ (CZG) and <em>Citrus grandis</em> Tomentosa (HZY). These enzymes displayed high substrate specificity for (2<em>S</em>)-eriodictyol. A strain capable of <em>de novo</em> synthesis of (2<em>S</em>)-hesperetin was developed by integrating the novel F4′OMTs and other biosynthetic pathway genes at high copy numbers into <em>Yarrowia lipolytica</em>. The engineered strain achieved a remarkable production titre of (2<em>S</em>)-hesperetin (130.2 mg/L), surpassing the yields of previously reported F4′OMTs. Furthermore, availability of the cofactor S-adenosylmethionine (SAM) was optimised to enhance methyltransferase catalytic efficiency, enabling the engineered strain to produce 178.2 mg/L of (2<em>S</em>)-hesperetin during fed-batch fermentation with SAM supplementation, the highest yield reported to date. This study represents the first successful <em>de novo</em> biosynthesis of (2<em>S</em>)-hesperetin in <em>Y. lipolytica</em>, providing valuable insights into the synthesis of other O-methylated flavonoids.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 728-736"},"PeriodicalIF":4.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776812","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

Optimized dual-AAV base editor delivery system with enhanced editing efficiency and virion production titer 优化了双aav碱基编辑器传递系统，提高了编辑效率和病毒粒子生产滴度

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-20 DOI: 10.1016/j.synbio.2025.03.007

Wenjia Yu , Yujie Wang , Siwei Li , Yingcai Dai , Yucheng Li , Xinyue Zhang , Bo Li , Siriguleng Qian , Xueli Zhang , Changhao Bi

{"title":"Optimized dual-AAV base editor delivery system with enhanced editing efficiency and virion production titer","authors":"Wenjia Yu , Yujie Wang , Siwei Li , Yingcai Dai , Yucheng Li , Xinyue Zhang , Bo Li , Siriguleng Qian , Xueli Zhang , Changhao Bi","doi":"10.1016/j.synbio.2025.03.007","DOIUrl":"10.1016/j.synbio.2025.03.007","url":null,"abstract":"<div><div>Base editors (BEs) are a promising tool for precise base conversion in human cells and animals, while the adeno-associated virus (AAV) is the major vector for human gene therapy. However, the size of the DNA cassette required for BE expression exceeds the 4.7 kb packing capacity of the AAV vector, making dual-AAV approaches based on <em>trans</em>-splicing intein necessary. Even with this approach, current split DNA cassettes are still larger than the AAV packing limit, posing a challenge for cellular production of AAV. Moreover, some split strategies yield variable editing results and target coverage. To address these limitations, 25 different split sets for BE4max and A3A-BE4max were tested at two target sites respectively, with splitting sites ranging from 493rd to 517th amino acids on the Cas9 peptide. Fortunately, the best Cas9 split site was identified between His511 and Ser512 and the arrangement of the AAV expression cassette was further manipulated to create evenly distributed CBE and ABE intein systems within 4.7 kb. These novel dual-AAV systems, designated 4.6AAV-CBE and 4.7AAV-ABE, were found to have base editing efficiencies similar to wild-type BEs, with a narrower editing window than the current 573 split system. Notably, 4.6AAV-CBE yield a higher AAV production titer, up to 2.1-fold in AAV-N and 1.5-fold in AAV-C, compared to the split-573BE system, likely due to the reduction of DNA cassette size within the AAV packaging capacity. Moreover, after packaging and infecting cells with AAV-N and AAV-C at the same volume and number of cells, the multiplicities of infection (MOI) and editing efficiency of 4.6 AAV-CBE were both higher than those of the split-573BE system. This study present advanced dual-AAV systems for ABE and CBE delivery, establishing a basis for safe and efficient BE therapies.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 697-706"},"PeriodicalIF":4.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776809","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

DNA storage: The future direction for medical cold data storage DNA存储：医学冷数据存储的未来方向

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-14 DOI: 10.1016/j.synbio.2025.03.006

Peilin Shen , Yukui Zheng , CongYu Zhang , Shuo Li , Yongru Chen , Yongsong Chen , Yuchen Liu , Zhiming Cai

{"title":"DNA storage: The future direction for medical cold data storage","authors":"Peilin Shen , Yukui Zheng , CongYu Zhang , Shuo Li , Yongru Chen , Yongsong Chen , Yuchen Liu , Zhiming Cai","doi":"10.1016/j.synbio.2025.03.006","DOIUrl":"10.1016/j.synbio.2025.03.006","url":null,"abstract":"<div><div>DNA storage, characterized by its durability, data density, and cost-effectiveness, is a promising solution for managing the increasing data volumes in healthcare.</div><div>This review explores state-of-the-art DNA storage technologies, and provides insights into designing a DNA storage system tailored for medical cold data. We anticipate that a practical approach for medical cold data storage will involve establishing regional, <em>in vitro</em> DNA storage centers that can serve multiple hospitals. The immediacy of DNA storage for medical data hinges on the development of novel, high-density, specialized coding methods. Established commercial techniques, such as DNA chemical synthesis and next-generation sequencing (NGS), along with mixed drying with alkaline salts and refined Polymerase Chain Reaction (PCR), potentially represent the optimal options for data writing, reading, storage, and accessing, respectively. Data security could be promised by the integration of traditional digital encryption and DNA steganography. Although breakthrough developments like artificial nucleotides and DNA nanostructures show potential, they remain in the laboratory research phase.</div><div>In conclusion, DNA storage is a viable preservation strategy for medical cold data in the near future.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 2","pages":"Pages 677-695"},"PeriodicalIF":4.4,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143759872","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

ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp ActinoMation：用于链霉菌属中通量机器人连接的识字编程方法

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-11 DOI: 10.1016/j.synbio.2025.03.005

Tenna A. Møller , Thomas J. Booth , Simon Shaw , Vilhelm K. Møller , Rasmus J.N. Frandsen , Tilmann Weber

{"title":"ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp","authors":"Tenna A. Møller , Thomas J. Booth , Simon Shaw , Vilhelm K. Møller , Rasmus J.N. Frandsen , Tilmann Weber","doi":"10.1016/j.synbio.2025.03.005","DOIUrl":"10.1016/j.synbio.2025.03.005","url":null,"abstract":"<div><div>The genus <em>Streptomyces</em> are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, have provided some access to the metabolic potential of <em>Streptomyces</em>, but efficient genetic engineering of strains is hindered by laborious and slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for the introduction of recombinant DNA into <em>Streptomyces</em> spp. using the affordable and open-sourced Opentrons (OT-2) robotics platform. To increase the accessibility of the workflow we provide an open-source protocol-creator, ActinoMation. ActinoMation is a literate programming environment using Python in Jupyter Notebook. We validated the method by transforming <em>Streptomyces coelicolor</em> (M1152 and M1146), <em>S. albidoflavus</em> (J1047), and <em>S. venezuelae</em> (DSM40230) with the plasmids pSETGUS and pIJ12551. We demonstrate conjugation efficiencies of 3.33∗10<sup>−3</sup>/0.33 % for M1152 with pSETGUS and pIJ12551; 2.96∗10<sup>−3</sup>/0.29 % for M1146 with pSETGUS and pIJ12551; 1.21∗10<sup>−5</sup>/0.0012 % for J1047 with pSETGUS and 4.70∗10<sup>−4</sup>/0.047 % with pIJ12551, and 4.97∗10<sup>−2</sup>/4.97 % for DSM40230 with pSETGUS and 6.13∗10<sup>−2</sup>/6.13 % with pIJ12551 with a false positive rate between 8.33 % and 54.54 %. Automation of the conjugation workflow facilitates a streamlined workflow on a larger scale without any evident loss of conjugation efficiency.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 2","pages":"Pages 667-676"},"PeriodicalIF":4.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143759098","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 production of hydroxysalidroside in Escherichia coli via enhanced glycosylation and semi-rational design of UGT85A1 通过增强糖基化和半合理设计UGT85A1在大肠杆菌中高效生产羟基皂苷

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-06 DOI: 10.1016/j.synbio.2025.03.002

Xinru Wang , Lian Wang , Qihang Chen , Ke Wang , Huijing Wang , Dong Li , Song Gao , Weizhu Zeng , Jingwen Zhou

{"title":"Efficient production of hydroxysalidroside in Escherichia coli via enhanced glycosylation and semi-rational design of UGT85A1","authors":"Xinru Wang , Lian Wang , Qihang Chen , Ke Wang , Huijing Wang , Dong Li , Song Gao , Weizhu Zeng , Jingwen Zhou","doi":"10.1016/j.synbio.2025.03.002","DOIUrl":"10.1016/j.synbio.2025.03.002","url":null,"abstract":"<div><div>Hydroxysalidroside is an important natural phenylethanoid glycoside with broad application prospects in the food and pharmaceutical fields. However, its low concentration in plants and complex extraction hinder its production. Despite being a promising way to synthesize hydroxysalidroside in <em>Escherichia coli</em>, glycosylation remains the limiting factor for its production. A <em>de novo</em> biosynthetic pathway for hydroxysalidroside was successfully constructed in <em>E. coli</em> via the screening of glycosyltransferase, overexpressing phosphoglucomutase (<em>pgm</em>) and UDP-glucose pyrophosphorylase (<em>galU</em>) to ensure a sufficient supply of UDP-glucose (UDPG). Additionally, a semi-rational design of <em>UGT85A1</em> was conducted to expand the acceptor-binding pocket to eliminate steric hindrance interfering with the binding of hydroxytyrosol. The endogenous genes <em>ushA</em> and <em>otsA</em> were knocked out to further reduce the consumption of UDPG. Finally, a titer of 5837.2 mg/L was achieved in a 5 L fermenter by optimizing the feeding times of carbon sources. This laid the foundation for the subsequent biosynthesis of phenylethanoid glycosides.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 2","pages":"Pages 638-649"},"PeriodicalIF":4.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620680","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

System-level characterization of engineered and evolved formatotrophic E. coli strains 工程和进化形成营养型大肠杆菌菌株的系统级特性

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-05 DOI: 10.1016/j.synbio.2025.03.001

Suzan Yilmaz , Boas Kanis , Rensco A.H. Hogers , Sara Benito-Vaquerizo , Jörg Kahnt , Timo Glatter , Beau Dronsella , Tobias J. Erb , Maria Suarez-Diez , Nico J. Claassens

{"title":"System-level characterization of engineered and evolved formatotrophic E. coli strains","authors":"Suzan Yilmaz , Boas Kanis , Rensco A.H. Hogers , Sara Benito-Vaquerizo , Jörg Kahnt , Timo Glatter , Beau Dronsella , Tobias J. Erb , Maria Suarez-Diez , Nico J. Claassens","doi":"10.1016/j.synbio.2025.03.001","DOIUrl":"10.1016/j.synbio.2025.03.001","url":null,"abstract":"<div><div>One-carbon compounds, such as formate, are promising and sustainable feedstocks for microbial bioproduction of fuels and chemicals. Growth of <em>Escherichia coli</em> on formate was recently achieved by introducing the reductive glycine pathway (rGlyP) into its genome, which is theoretically the most energy-efficient aerobic formate assimilation pathway. While adaptive laboratory evolution was used to enhance the growth rate and biomass yield significantly, still the best performing formatotrophic <em>E. coli</em> strain did not approach the theoretical optimal biomass yield of the rGlyP. In this study, we investigated these previously engineered formatotrophic <em>E. coli</em> strains to find out why the biomass yield was sub-optimal and how it may be improved. Through a combination of metabolic modelling, genomic and proteomic analysis, we identified several potential metabolic bottlenecks and future targets for optimization. This study also reveals further insights in the evolutionary mutations and related changes in proteome allocation that supported the already substantially improved growth of formatotrophic <em>E. coli</em> strains. This systems-level analysis provides key insights to realize high-yield, fast growing formatotrophic strains for future bioproduction.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 2","pages":"Pages 650-666"},"PeriodicalIF":4.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143637249","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

CRISPR/Cas9-based iterative multi-copy integration for improved metabolite yields in Saccharomyces cerevisiae 基于CRISPR/ cas9的迭代多拷贝整合提高酿酒酵母代谢物产量

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-03-03 DOI: 10.1016/j.synbio.2025.02.016

Ximei Chen , Chenyang Li , Xin Qiu , Ming Chen , Yongping Xu , Shuying Li , Qian Li , Liang Wang

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