Microbial Biotechnology最新文献_第9页

Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440 进化工程辅助下的理性设计允许恶臭假单胞菌KT2440复杂表型的构建和优化

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-24 DOI: 10.1111/1751-7915.70132

Blas Blázquez, Juan Nogales

{"title":"Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440","authors":"Blas Blázquez, Juan Nogales","doi":"10.1111/1751-7915.70132","DOIUrl":"https://doi.org/10.1111/1751-7915.70132","url":null,"abstract":"Beyond the rational construction of genetic determinants to encode target functions, complex phenotype engineering requires the contextualisation of their expression within the metabolic and genetic background of the host strain. Furthermore, wherever metabolic complexity is involved, phenotype engineering demands standard, reliable, plug-and-play tools. We introduce GENIO (GENome Integration and fitness Optimization platform for Pseudomonas putida), a framework to optimise genetic circuit performance by means of (i) chromosome-location-based differential gene expression and (ii) subsequent fitness improvement through evolutionary engineering if needed. Using gene expression strength and cell-to-cell variation, we characterised 10 P. putida chromosomal loci (ppLPS) to show that genome context rather than distance to ORI is the main factor driving differential expression performance. We further contextualised ppLPS gene expression against well-known chromosomal integration sites and plasmids displaying different copy numbers. GENIO supports comprehensive exploration of the gene expression space across P. putida's genome while unlocking performance optimization of complex heterologous metabolic pathways through evolutionary engineering. To demonstrate the usability of GENIO, we restored P. putida's aromatic hydrocarbon metabolism by (de)constructing the toluene/m-xylene catabolic pathway coded in the pWW0 plasmid. We also showed that engineering complex phenotypes requires accurate contextualisation of the synthetic pathways involved, a process that benefits from biological robustness.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689942","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

Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440 进化工程辅助下的理性设计允许恶臭假单胞菌KT2440复杂表型的构建和优化

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-24 DOI: 10.1111/1751-7915.70132

Blas Blázquez, Juan Nogales

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引用次数: 0

Semirational Design of SenC to Enhance Organic Selenium Biosynthesis 促进有机硒生物合成的SenC半设计。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-22 DOI: 10.1111/1751-7915.70130

Kailin Shao, Xiaobin Yu, Yan Zhao, Ying Zhang, Xiaobo Liu

引用次数: 0

Model-Driven Engineering of Yarrowia lipolytica for Improved Microbial Oil Production 提高微生物采油效率的脂质体耶氏菌模型驱动工程。

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-20 DOI: 10.1111/1751-7915.70089

Zeynep Efsun Duman-Özdamar, Mattijs K. Julsing, Vitor A. P. Martins dos Santos, Jeroen Hugenholtz, Maria Suarez-Diez

{"title":"Model-Driven Engineering of Yarrowia lipolytica for Improved Microbial Oil Production","authors":"Zeynep Efsun Duman-Özdamar, Mattijs K. Julsing, Vitor A. P. Martins dos Santos, Jeroen Hugenholtz, Maria Suarez-Diez","doi":"10.1111/1751-7915.70089","DOIUrl":"10.1111/1751-7915.70089","url":null,"abstract":"Extensive usage of plant-based oils, especially palm oil, has led to environmental and social issues, such as deforestation and loss of biodiversity, thus sustainable alternatives are required. Microbial oils, especially from Yarrowia lipolytica, offer a promising solution because of their similar composition to palm oil, low carbon footprint and ability to utilise low-cost substrates. In this study, we employed the Design-Build-Test-Learn (DBTL) approach to enhance lipid production in Y. lipolytica. We systematically evaluated predictions from the genome-scale metabolic model to identify and overcome bottlenecks in lipid biosynthesis. We tested the effect of predicted medium supplements (glutamate, leucine, methionine and threonine) and genetic intervention targets, including the overexpression of ATP-citrate lyase (ACL), acetyl-CoA carboxylase (ACC), threonine synthase (TS), diacylglycerol acyltransferase(DGA1), the deletion of citrate exporter gene (CEX1) and disruption of β-oxidation pathway (MFE1). This work revealed the critical roles of ACC, ACL, TS and DGA1 and the interaction of these genes with elevated intracellular citrate availability in lipid biosynthesis. Combining TS and DGA1 overexpression in the Δmfe_Δcex background achieved a remarkable 200% increase in lipid content (56% w/w) and a 230% increase in lipid yield on glycerol. These findings underscore the potential of Y. lipolytica as an efficient microbial cell factory for fatty acid production. Our study advances the understanding of lipid metabolism in Y. lipolytica and demonstrates a viable approach for developing sustainable and economically feasible alternatives to palm oil.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668615","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

Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications 由人工智能增强的微生物技术用于医疗保健应用

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-18 DOI: 10.1111/1751-7915.70131

Taeho Yu, Minjee Chae, Ziling Wang, Gahyeon Ryu, Gi Bae Kim, Sang Yup Lee

引用次数: 0

Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications 由人工智能增强的微生物技术用于医疗保健应用

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-18 DOI: 10.1111/1751-7915.70131

Taeho Yu, Minjee Chae, Ziling Wang, Gahyeon Ryu, Gi Bae Kim, Sang Yup Lee

引用次数: 0

Engineering Xylose Isomerase and Reductase Pathways in Yarrowia lipolytica for Efficient Lipid Production 工程木糖异构酶和还原酶途径在解脂耶氏菌高效脂质生产

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-14 DOI: 10.1111/1751-7915.70127

Isabel De La Torre, Miguel G. Acedos, Juan J. Cestero, Jorge Barriuso, José L. García

{"title":"Engineering Xylose Isomerase and Reductase Pathways in Yarrowia lipolytica for Efficient Lipid Production","authors":"Isabel De La Torre, Miguel G. Acedos, Juan J. Cestero, Jorge Barriuso, José L. García","doi":"10.1111/1751-7915.70127","DOIUrl":"https://doi.org/10.1111/1751-7915.70127","url":null,"abstract":"Xylose is a common monosaccharide in lignocellulosic residues that Yarrowia lipolytica cannot naturally metabolise for lipid production and therefore, heterologous xylose metabolic pathways must be engineered in this yeast to facilitate its consumption. We have compared the metabolic efficiency of two xylose metabolic pathways by developing three recombinant Y. lipolytica strains: one harbouring a xylose reductase pathway, one with a xylose isomerase pathway, and one combining both pathways, and the strains were tested for xylose consumption and lipid production at different scales. The recombinant strain with the reductase pathway that was directly isolated in selective xylose medium showed the highest lipid yield, producing up to 12.8 g/L of lipids, or 43% of the biomass dry weight, without requiring any other xylose consumption adaptive evolution process. This strain achieved a lipid yield of 0.13 g lipids/g xylose, one of the highest yields in yeast reported so far using xylose as the sole carbon and energy source. Although the strain harbouring the isomerase pathway performed better under oxygen-limiting conditions and led to higher lipid intracellular accumulation, it showed a lower xylose uptake and biomass production, rendering a lower yield under non-limiting oxygen conditions. Unexpectedly, the combination of both pathways in the same strain was less effective than the use of the reductase pathway alone.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70127","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629813","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

Engineering Xylose Isomerase and Reductase Pathways in Yarrowia lipolytica for Efficient Lipid Production 工程木糖异构酶和还原酶途径在解脂耶氏菌高效脂质生产

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-14 DOI: 10.1111/1751-7915.70127

Isabel De La Torre, Miguel G. Acedos, Juan J. Cestero, Jorge Barriuso, José L. García

{"title":"Engineering Xylose Isomerase and Reductase Pathways in Yarrowia lipolytica for Efficient Lipid Production","authors":"Isabel De La Torre, Miguel G. Acedos, Juan J. Cestero, Jorge Barriuso, José L. García","doi":"10.1111/1751-7915.70127","DOIUrl":"https://doi.org/10.1111/1751-7915.70127","url":null,"abstract":"Xylose is a common monosaccharide in lignocellulosic residues that Yarrowia lipolytica cannot naturally metabolise for lipid production and therefore, heterologous xylose metabolic pathways must be engineered in this yeast to facilitate its consumption. We have compared the metabolic efficiency of two xylose metabolic pathways by developing three recombinant Y. lipolytica strains: one harbouring a xylose reductase pathway, one with a xylose isomerase pathway, and one combining both pathways, and the strains were tested for xylose consumption and lipid production at different scales. The recombinant strain with the reductase pathway that was directly isolated in selective xylose medium showed the highest lipid yield, producing up to 12.8 g/L of lipids, or 43% of the biomass dry weight, without requiring any other xylose consumption adaptive evolution process. This strain achieved a lipid yield of 0.13 g lipids/g xylose, one of the highest yields in yeast reported so far using xylose as the sole carbon and energy source. Although the strain harbouring the isomerase pathway performed better under oxygen-limiting conditions and led to higher lipid intracellular accumulation, it showed a lower xylose uptake and biomass production, rendering a lower yield under non-limiting oxygen conditions. Unexpectedly, the combination of both pathways in the same strain was less effective than the use of the reductase pathway alone.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70127","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629812","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 Metabolic and Physiological Responses to Spaceflight of a Lipopeptide-Producing Bacillus subtilis 产脂肽枯草芽孢杆菌在太空中的代谢和生理反应

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-13 DOI: 10.1111/1751-7915.70111

Wan-Qi Qin, Yi-Fan Liu, Jin-Feng Liu, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu

{"title":"The Metabolic and Physiological Responses to Spaceflight of a Lipopeptide-Producing Bacillus subtilis","authors":"Wan-Qi Qin, Yi-Fan Liu, Jin-Feng Liu, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu","doi":"10.1111/1751-7915.70111","DOIUrl":"https://doi.org/10.1111/1751-7915.70111","url":null,"abstract":"Outer space is an extreme environment and the survival of many microorganisms after spaceflight is well established. However, adaptations of Bacillus subtilis to space stress, particularly metabolism, are largely unknown. Here, we first performed a spaceflight mission of the B. subtilis TD7 strain and compared the spaceflight-exposed strain with the wild-type in terms of their phenotype, biofilm formation and secondary metabolism. The spaceflight-exposed strain exhibited slower growth, different morphology and decreased biofilm formation. Importantly, a decline in lipopeptide production was observed after spaceflight. Multi-omics approaches were used to uncover the molecular mechanisms underlying secondary metabolism and 997 differentially expressed genes (DEGs) were found, involving the TCA cycle, fatty acid degradation, amino acid biosynthesis and quorum sensing systems. Further analysis of 26 lipopeptide-related DEGs further elucidated the relationship between the space environment and secondary metabolism regulation. Our findings could contribute to a better understanding of the relationship between the space environment and microbial adaptation mechanisms.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143602467","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 Metabolic and Physiological Responses to Spaceflight of a Lipopeptide-Producing Bacillus subtilis 产脂肽枯草芽孢杆菌在太空中的代谢和生理反应

IF 5.7 2区生物学

Microbial Biotechnology Pub Date : 2025-03-13 DOI: 10.1111/1751-7915.70111

Wan-Qi Qin, Yi-Fan Liu, Jin-Feng Liu, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu

{"title":"The Metabolic and Physiological Responses to Spaceflight of a Lipopeptide-Producing Bacillus subtilis","authors":"Wan-Qi Qin, Yi-Fan Liu, Jin-Feng Liu, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu","doi":"10.1111/1751-7915.70111","DOIUrl":"https://doi.org/10.1111/1751-7915.70111","url":null,"abstract":"Outer space is an extreme environment and the survival of many microorganisms after spaceflight is well established. However, adaptations of Bacillus subtilis to space stress, particularly metabolism, are largely unknown. Here, we first performed a spaceflight mission of the B. subtilis TD7 strain and compared the spaceflight-exposed strain with the wild-type in terms of their phenotype, biofilm formation and secondary metabolism. The spaceflight-exposed strain exhibited slower growth, different morphology and decreased biofilm formation. Importantly, a decline in lipopeptide production was observed after spaceflight. Multi-omics approaches were used to uncover the molecular mechanisms underlying secondary metabolism and 997 differentially expressed genes (DEGs) were found, involving the TCA cycle, fatty acid degradation, amino acid biosynthesis and quorum sensing systems. Further analysis of 26 lipopeptide-related DEGs further elucidated the relationship between the space environment and secondary metabolism regulation. Our findings could contribute to a better understanding of the relationship between the space environment and microbial adaptation mechanisms.","PeriodicalId":209,"journal":{"name":"Microbial Biotechnology","volume":"18 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1751-7915.70111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143602567","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