Synthetic and Systems Biotechnology最新文献

Engineering T7 RNA polymerase-cascaded systems controlled by nisin and theophylline for protein overexpression and targeted gene mutagenesis in Lactococcus lactis 乳酸菌蛋白和茶碱控制的T7 RNA聚合酶级联系统在乳酸乳球菌中的蛋白过表达和靶向基因诱变

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-22 DOI: 10.1016/j.synbio.2025.06.008

Ying Huang , Kang Ma , Yan Li , Qingyan Li , Fuping Lu , Xueli Zhang , Zhe Sun

{"title":"Engineering T7 RNA polymerase-cascaded systems controlled by nisin and theophylline for protein overexpression and targeted gene mutagenesis in Lactococcus lactis","authors":"Ying Huang , Kang Ma , Yan Li , Qingyan Li , Fuping Lu , Xueli Zhang , Zhe Sun","doi":"10.1016/j.synbio.2025.06.008","DOIUrl":"10.1016/j.synbio.2025.06.008","url":null,"abstract":"<div><div><em>Lactococcus lactis</em> serves as an important platform for heterologous protein production, with the nisin-controlled gene expression (NICE) system being widely employed for regulated protein overexpression. However, the NICE system relies on the native RNA polymerase, which limits transcriptional efficiency, and there remains a lack of tools enabling continuous target gene mutagenesis in <em>L. lactis</em>. In this study, we enhanced the NICE system by integrating the highly processive T7 RNA polymerase (T7RNAP) to boost protein expression. A theophylline-dependent riboswitch, RbxE, was incorporated into the nisin-induced promoter to mitigate the toxicity caused by basal T7RNAP expression in <em>Escherichia coli</em>. Directed mutagenesis of the riboswitch region between the stem-loop and the ribosome binding site optimized T7RNAP expression, leading to a 2.4-fold increase upon nisin and theophylline induction in <em>L. lactis.</em> The resulting NICE-T7 system achieved a 2.8-fold increase in GFP compared to the original NICE system. Furthermore, adenosine deaminase TadA8e was fused to T7RNAP to generate the MutaT7LL system, facilitating targeted A-to-G mutagenesis and successfully reactivated an erythromycin resistance gene with a mutation efficiency of 1.33 × 10<sup>−6</sup>. Overall, this study presents an upgraded NICE system that enhances protein production and enables continuous in vivo mutagenesis of target genes in <em>L. lactis</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1150-1159"},"PeriodicalIF":4.4,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144501319","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

Decoding yeast transcriptional regulation via a data-and mechanism-driven distributed large-scale network model 通过数据和机制驱动的分布式大规模网络模型解码酵母转录调控

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-14 DOI: 10.1016/j.synbio.2025.06.005

Xingcun Fan , Guangming Xiang , Wenbin Liao , Luchi Xiao , Siwei He , Na Luo , Hongzhong Lu , Xuefeng Yan

{"title":"Decoding yeast transcriptional regulation via a data-and mechanism-driven distributed large-scale network model","authors":"Xingcun Fan , Guangming Xiang , Wenbin Liao , Luchi Xiao , Siwei He , Na Luo , Hongzhong Lu , Xuefeng Yan","doi":"10.1016/j.synbio.2025.06.005","DOIUrl":"10.1016/j.synbio.2025.06.005","url":null,"abstract":"<div><div>The complex transcriptional regulatory relationships among genes influence gene expression levels and play a crucial role in determining cellular phenotypes. In this study, we propose a novel, distributed, large-scale transcriptional regulatory neural network model (DLTRNM), which integrates prior knowledge into the reconstruction of pre-trained machine learning models, followed by fine-tuning. Using <em>Saccharomyces cerevisiae</em> as a case study, the curated transcriptional regulatory relationships are used to define the interactions between transcription factors (TFs) and their target genes (TGs). Subsequently, DLTRNM is pre-trained on pan-transcriptomic data and fine-tuned with time-series data, enabling it to accurately predict regulatory correlations. Additionally, DLTRNM can help identify potential key TFs, thereby simplifying the complex and interrelated transcriptional regulatory networks (TRNs). It can also complement previously reported transcriptional regulatory subnetworks. DLTRNM provides a powerful tool for studying transcriptional regulation with reduced computational demands and enhanced interpretability. Thus, this study marks a significant advancement in systems biology for understanding the complex transcriptional regulation within cells.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1140-1149"},"PeriodicalIF":4.4,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144492172","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

Genomic and transcriptomic insights into the molecular responses of a biocrust-derived oleaginous microalga Vischeria sp. WL1 to nitrogen depletion and recovery 生物外壳衍生的产油微藻Vischeria sp. WL1对氮消耗和恢复的分子反应的基因组学和转录组学见解

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-14 DOI: 10.1016/j.synbio.2025.06.004

Xiaolan Rao , Wensheng Liang , Xin Jing , Chang Liu , Jiahong Li , Limei Liu , Xiang Gao

{"title":"Genomic and transcriptomic insights into the molecular responses of a biocrust-derived oleaginous microalga Vischeria sp. WL1 to nitrogen depletion and recovery","authors":"Xiaolan Rao , Wensheng Liang , Xin Jing , Chang Liu , Jiahong Li , Limei Liu , Xiang Gao","doi":"10.1016/j.synbio.2025.06.004","DOIUrl":"10.1016/j.synbio.2025.06.004","url":null,"abstract":"<div><div>Microalgae surviving in extreme conditions evolve tolerance mechanisms to diverse environmental stresses. Environmental nitrogen limitation or nitrogen starvation poses a significant threat to the growth of microalgae, but it is an effective factor in inducing lipid accumulation in many microalgal species. In this study, we report the genome sequence of a promising oil-producing strain, <em>Vischeria</em> sp. WL1, which is capable of resisting long-term nitrogen starvation and responds rapidly to nitrogen recovery. Its genome comprises 127 Mb of nuclear DNA and 17,392 protein-coding genes. Comparative genomic and transcriptomic analyses identified a group of genes involved in nitrate metabolism and lipid accumulation. Heterologous expression of three candidate genes in the model cyanobacterium <em>Synechocystis</em> sp. PCC 6803 demonstrated their effects on restoring the cellular chlorophyll upon nitrogen recovery. Our results provide novel insights into the molecular basis of metabolic shifts in response to nitrogen starvation and recovery in microalgae.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1160-1171"},"PeriodicalIF":4.4,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144501320","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

Metabolic engineering of Escherichia coli for squalene overproduction 过量生产角鲨烯的大肠杆菌代谢工程

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-07 DOI: 10.1016/j.synbio.2025.06.003

Jiangming Zhu , Yaping Mao , Hongchun Mo , Xuehui Dai , Yuhan Wu , Guangyi Wang , Zhanguang Feng , Ruirui Yue , Dongzhi Wei , Haili Liu , Yong Wang

{"title":"Metabolic engineering of Escherichia coli for squalene overproduction","authors":"Jiangming Zhu , Yaping Mao , Hongchun Mo , Xuehui Dai , Yuhan Wu , Guangyi Wang , Zhanguang Feng , Ruirui Yue , Dongzhi Wei , Haili Liu , Yong Wang","doi":"10.1016/j.synbio.2025.06.003","DOIUrl":"10.1016/j.synbio.2025.06.003","url":null,"abstract":"<div><div>Squalene, a lipophilic triterpene with multifaceted bioactivities, faces bioproduction bottlenecks in microbial hosts due to inefficient biosynthetic pathways and limited storage capacity. Here, we address these challenges through systems metabolic engineering integrating redox-balanced 3-hydroxy-3-methyl glutaryl coenzyme A reductase (HMGR) variants and membrane lipid remodeling. By developing a hybrid HMGRs system combining NADPH-dependent and NADH-preferred enzymes, squalene production reached 852.06 ± 28.95 mg/L with balanced cofactor utilization. Subsequent engineering of membrane morphology and lipid metabolism generated lipid-enriched elongated cells, through the overexpression of <em>dgs</em>, <em>murG</em> and <em>plsC</em>, boosting squalene production to 970.86 ± 55.67 mg/L. Implementation of delayed induction strategies coupled with 10 % dodecane overlay as an <em>in situ</em> recovery system achieved a final squalene titer of 1267.01 mg/L in a 3 L bioreactor. Mechanistic studies revealed fatty acid (FA) and phosphatidylethanolamine (PE) as key reservoirs for squalene in <em>E</em>. <em>coli</em>, with <em>dgs</em> overexpression specifically promoting cellular elongation. This article provides comprehensive insights into engineering strategies and mechanistic perspectives, establishing a universal framework for hydrophobic metabolite biomanufacturing in prokaryotic hosts.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1119-1126"},"PeriodicalIF":4.4,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314259","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

Improving fidaxomicin production through ARTP mutagenesis and fermentation optimization in Actinoplanes deccanensis 通过ARTP诱变和发酵优化提高非达霉素的产量

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-07 DOI: 10.1016/j.synbio.2025.06.002

Jing-Yi Ruan , Huang Xie , Yi-Lei Zheng , Qing-Wei Zhao , Xin-Ai Chen , Zhong-Yuan Lyu , Yong-Quan Li

{"title":"Improving fidaxomicin production through ARTP mutagenesis and fermentation optimization in Actinoplanes deccanensis","authors":"Jing-Yi Ruan , Huang Xie , Yi-Lei Zheng , Qing-Wei Zhao , Xin-Ai Chen , Zhong-Yuan Lyu , Yong-Quan Li","doi":"10.1016/j.synbio.2025.06.002","DOIUrl":"10.1016/j.synbio.2025.06.002","url":null,"abstract":"<div><div>Fidaxomicin, a macrolide antibiotic, is widely used to treat <em>Clostridioides difficile</em> infection (CDI). It demonstrats significantly higher clinical efficacy than vancomycin and metronidazole. However, the large-scale industrial production of it remains a significant challenge because of the low fermentation yields. In this study, we chosen the strain OE-R1/WT as the starting strain, in which a pathway-specific positive regulatory factor <em>fadR1</em> was overexpressed. By using the <em>kanR/gusA</em> dual-reporter system and ARTP mutagenesis, we screened a high-yield strain, PA-13, which produced 757.34 mg/L of fidaxomicin, representing a 5.5-fold increase over OE-R1/WT and having enhanced genetic stability. Furthermore, by overexpressing two methyltransferases within the biosynthetic cluster and supplementing with exogenous DMSO, we further increased the production of fidaxomicin to 929.17 mg/L, while reducing the accumulation of the major by-product to 20.9 %. Finally, through the optimization of fermentation strategies at both the shake flask and 15 L fermenter levels, we achieved a final yield of 3949.05 mg/L in the 15 L fermenter, which represents the highest yield up to date. Our study represents the first successful enhancement of fidaxomicin production in <em>Actinoplanes deccanensis</em> to over 3.9 g/L in a 15 L fermenter, establishing a robust foundation for industrial-scale fermentation. Additionally, it provides significant insights for the development of high-yield strains in other actinomycetes.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1098-1106"},"PeriodicalIF":4.4,"publicationDate":"2025-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144271523","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

Enhancing 3-hydroxypropionic acid production from recombinant Saccharomyces cerevisiae for using rice straw hydrolysate and sugar cane industrial waste as substrate 以水稻秸秆水解液和甘蔗工业废料为底物，提高重组酿酒酵母生产3-羟基丙酸的能力

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-06-01 DOI: 10.1016/j.synbio.2025.05.011

Supattra Lertsriwong , Phatcharaphong Khaosaart , Nassapat Boonvitthya , Warawut Chulalaksananukul , Chompunuch Glinwong

{"title":"Enhancing 3-hydroxypropionic acid production from recombinant Saccharomyces cerevisiae for using rice straw hydrolysate and sugar cane industrial waste as substrate","authors":"Supattra Lertsriwong , Phatcharaphong Khaosaart , Nassapat Boonvitthya , Warawut Chulalaksananukul , Chompunuch Glinwong","doi":"10.1016/j.synbio.2025.05.011","DOIUrl":"10.1016/j.synbio.2025.05.011","url":null,"abstract":"<div><div>Rice straw and sugar cane industrial waste are a plentiful source of lignocellulosic biomass with a high polysaccharide content, that is hydrolyzed into sugar for microbial growth and their metabolites. 3-Hydroxypropionic acid (3-HP) is a promising chemical building block that can be produced from renewable resources. The malonyl-CoA pathway is one of the biosynthetic routes for 3-HP production by expressing the malonyl-CoA reductase gene (<em>mcr</em>). However, the problem of the activity imbalance between the C and N-terminal causes a low conversion rate of malonyl-CoA to 3-hydroxypropionic acid. This study aimed to balance the bi-functional MCR enzyme by dissecting MCR into two fragments and enhancing the supply of intermediates to increase the production of 3-HP. The recombinant strain harboring the dissected <em>mcr</em> gene showed a 21-fold increase in 3-HP titer compared to the strain carrying the full-length <em>mcr</em> gene. The addition of cerulenin and acetate to the fermented medium enhanced 3-HP yield by 8 times, in which recombinant yeast produced 3-HP up to 10 g/L (0.201 g<sub>product</sub>/g<sub>substrate</sub>). The results of using rice straw hydrolysate as a carbon source indicated that <em>Saccharomyces cerevisiae</em> S2 produced 3-HP of 4.02 g/L, which was 0.074 g<sub>product</sub>/g<sub>glucose</sub> in the diluted hydrolysate. These findings provide an alternative and sustainable strategy for utilizing lignocellulosic biomass for future 3-HP production at an industrial scale.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1077-1086"},"PeriodicalIF":4.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261826","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

Construction of a genome-engineered stable 5-aminolevulinic acid producing Corynebacterium glutamicum by increasing succinyl-CoA supply 通过增加琥珀酰辅酶a供应构建基因组工程稳定的5-氨基乙酰丙酸产谷氨酸棒状杆菌

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-05-30 DOI: 10.1016/j.synbio.2025.05.013

Yangyang Zheng , Ziyao Wang , Jianbo Li , Zhouxiao Geng , Tao Chen , Zhiwen Wang

{"title":"Construction of a genome-engineered stable 5-aminolevulinic acid producing Corynebacterium glutamicum by increasing succinyl-CoA supply","authors":"Yangyang Zheng , Ziyao Wang , Jianbo Li , Zhouxiao Geng , Tao Chen , Zhiwen Wang","doi":"10.1016/j.synbio.2025.05.013","DOIUrl":"10.1016/j.synbio.2025.05.013","url":null,"abstract":"<div><div>5-Aminolevulinic acid (5-ALA), a versatile precursor for tetrapyrrole derivatives (such as heme, chlorophyll, and cobalamin), drives advancing microbial cell factories to meet growing biomedical and industrial demands. However, there remain two challenges that limit yield and scalability: the limitations of conventional plasmid-based gene expression systems and the lack of fine regulation of succinyl-CoA. In this study, to address these limitations, we integrated multiple copies of <em>hemA</em><sup><em>C132A</em></sup> of the heterologous C4 pathway on the genome. For fine regulating the supply of succinyl-CoA, the genes related to the tricarboxylic acid cycle (TCA cycle) oxidation branch pathway were combinatorially screened. The optimal combination of <em>icd</em> and <em>lpd</em> was confirmed by ribosome binding site (RBS) engineering, which was integrated on the genome with optimized expression intensity. Succinyl-CoA supply was further increased by genome integration and expression optimization of key CoA biosynthetic gene <em>coaA</em>, pantothenic acid synthesis-related gene <em>panB-panC</em>, and β-alanine synthesis-related gene <em>panD</em>. The optimized genomically stable chassis achieved a high 5-ALA production of 6.38 ± 0.16 g/L, which was 8.63-fold higher than the single <em>hemA</em><sup><em>C132A</em></sup> copy strain A1 (0.74 ± 0.07 g/L). From these findings, a stable and high-yield 5-ALA synthetic strain was successfully constructed, providing a new strategy for production of biochemicals derived from succinyl-CoA in <em>C. glutamicum</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1070-1076"},"PeriodicalIF":4.4,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144240859","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

Systematic design and evaluation of artificial CO2 assimilation pathways 人工CO2同化途径的系统设计与评价

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-05-28 DOI: 10.1016/j.synbio.2025.05.009

Yushuo Liu , Guangyun Chu , Xiaoming Dong , Hao Luo , Zhitao Mao , Yufeng Mao , Qianqian Yuan , Hongwu Ma

{"title":"Systematic design and evaluation of artificial CO2 assimilation pathways","authors":"Yushuo Liu , Guangyun Chu , Xiaoming Dong , Hao Luo , Zhitao Mao , Yufeng Mao , Qianqian Yuan , Hongwu Ma","doi":"10.1016/j.synbio.2025.05.009","DOIUrl":"10.1016/j.synbio.2025.05.009","url":null,"abstract":"<div><div>With the advancement of industry and bio-agriculture, the effective management of CO<sub>2</sub> has emerged as a critical challenge for humanity. This study systematically explores multiple CO<sub>2</sub> assimilation pathways using the comb-FBA algorithm, aiming to identify efficient artificial carbon fixation pathways. By extracting 49 CO<sub>2</sub> and HCO<sub>3</sub><sup>−</sup> involved reactions and combining them with 6,529 reactions from MetaCyc, we constructed the computational set for analysis. These 16 core reactions give rise to 136 carbon fixation pathways for single C<sub>2</sub> targets (such as acetyl-CoA, glyoxylate, and oxalate) and 576 carbon fixation pathways for single C<sub>3</sub> targets (including glyceraldehyde-3-phosphate or pyruvate). Based on these core reactions, we identified four principal carbon fixation modes. Through systematic assessments, we identified 12 promising CO<sub>2</sub> fixation pathways, each comprising no more than 20 reaction steps and demonstrating thermodynamic feasibility. Through further analysis of enzyme oxygen sensitivity and availability, we identified three novel and promising pathways. By examining metabolite conversion relationships, we also identified alternative carbon fixation reaction modules, offering flexibility for pathway optimization and experimental design. In conclusion, this study provides a diverse library of artificial carbon fixation pathways, demonstrating the power of the comb-FBA algorithm in designing carbon assimilation pathways and laying the foundation for more efficient CO<sub>2</sub> fixation strategies.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 4","pages":"Pages 1107-1118"},"PeriodicalIF":4.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314260","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

Construction of a synthetic biology toolkit for the genetic manipulation in the cellulose-producing strain Kosakonia oryzendophytica 纤维素产菌稻谷内生菌遗传操作合成生物学工具包的构建

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-05-27 DOI: 10.1016/j.synbio.2025.05.012

Liangtian Miao , Wei Feng , Jiaxun Ren , Keke Sun , Guoqiang Li , Huifeng Jiang

{"title":"Construction of a synthetic biology toolkit for the genetic manipulation in the cellulose-producing strain Kosakonia oryzendophytica","authors":"Liangtian Miao , Wei Feng , Jiaxun Ren , Keke Sun , Guoqiang Li , Huifeng Jiang","doi":"10.1016/j.synbio.2025.05.012","DOIUrl":"10.1016/j.synbio.2025.05.012","url":null,"abstract":"<div><div>Bacterial cellulose (BC), a robust and highly crystalline nanomaterial composed of glucose polymers, exhibits exceptional properties including superior water retention capacity, biocompatibility, and customizable mechanical strength, positioning it as a promising candidate for advanced material applications. To harness its full potential, we developed a synthetic biology platform for engineering <em>Kosakonia oryzendophytica</em>—a hyperproductive BC synthesis strain. First, we systematically characterized a library of regulatory elements (promoters, ribosome binding sites, and terminators, etc.) in this chassis, demonstrating tunable expression intensities ranging from 1.84 % to 169 % relative to the canonical <em>LacO1</em> promoter. Subsequently, we established a high-efficiency CRISPR/Cas9-mediated scarless genome editing system through coordinated optimization of λ Red recombinase and Cas9 nuclease expression, achieving near-perfect editing efficiency (≈100 %). This system was functionally validated by targeted knockout of key genes (<em>bcsA</em>, <em>fbp</em>, and <em>galU</em>), with scanning electron microscopy analysis confirming the BC synthesis deficiency in Δ<em>bcsA</em> and Δ<em>fbp</em> mutants. The integration of these genetic tools—comprising tunable expression modules and precision genome-editing capabilities—provides a comprehensive toolkit for reprogramming <em>K. oryzendophytica</em> to produce next-generation cellulose-based functional materials with tailored properties.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1050-1058"},"PeriodicalIF":4.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223373","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

Morphology-engineered alleviation of mycelial aggregation in Streptomyces chassis for potentiated production of secondary metabolites 形态工程减轻链霉菌的菌丝聚集，以增强次生代谢物的产生

IF 4.4 2区生物学

Synthetic and Systems Biotechnology Pub Date : 2025-05-26 DOI: 10.1016/j.synbio.2025.05.010

Shuo Liu , Fei Xiao , Lanxin Lv , Meiyan Wang , Wenli Li , Guoqing Niu

{"title":"Morphology-engineered alleviation of mycelial aggregation in Streptomyces chassis for potentiated production of secondary metabolites","authors":"Shuo Liu , Fei Xiao , Lanxin Lv , Meiyan Wang , Wenli Li , Guoqing Niu","doi":"10.1016/j.synbio.2025.05.010","DOIUrl":"10.1016/j.synbio.2025.05.010","url":null,"abstract":"<div><div>The genus <em>Streptomyces</em> exhibits a complex life cycle of morphological differentiation and an extraordinary capacity to produce numerous bioactive secondary metabolites. In submerged cultures, <em>Streptomyces</em> species usually grow in the form of mycelial networks and aggregate into large pellets or clumps, which is generally unfavorable for industrial production. This study aimed to construct efficient microbial cell factories by manipulating morphology-related genes. We herein employed a morphology engineering approach to generate eight engineered derivatives (MECS01∼MECS08) of <em>Streptomyces coelicolor</em> M1146, a versatile chassis widely used for the heterologous production of various secondary metabolites. We found that genetic manipulation of morphology-related genes exerted a substantial influence on the growth and mycelial characteristics of the engineered strains. Once the native actinorhodin gene cluster was introduced into these strains, antibiotic production increased in all engineered strains compared to the parental strain. Notably, a significant elevation of actinorhodin production was observed in three of the engineered strains, MECS01, MECS03 and MECS05. Similar scenarios occurred when expressing the staurosporine gene cluster and the carotenoid gene cluster in these three engineered derivatives, respectively. Our study demonstrates that morphology engineering represents an effective strategy for alleviating mycelial aggregation. It has also expanded the toolkit of <em>Streptomyces</em> chassis available for the heterologous expression of gene clusters encoding a variety of secondary metabolites.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1059-1069"},"PeriodicalIF":4.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230010","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