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Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli. 一种基于适体体的细胞内荧光生物传感器的设计，用于跟踪大肠杆菌的负荷。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-07-02 DOI: 10.1016/j.tibtech.2025.06.007
Alice Grob, Tom Copeman, Sifeng Chen, Jacopo Gabrielli, Yuval Elani, Elisa Franco, Francesca Ceroni
{"title":"Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.","authors":"Alice Grob, Tom Copeman, Sifeng Chen, Jacopo Gabrielli, Yuval Elani, Elisa Franco, Francesca Ceroni","doi":"10.1016/j.tibtech.2025.06.007","DOIUrl":"10.1016/j.tibtech.2025.06.007","url":null,"abstract":"<p><p>Cell burden impacts the performance of engineered genetic constructs with great interest towards the development of tools to track it and improve biotechnology applications. Fluorogenic RNA aptamers are excellent candidates for live monitoring of burden because their production is expected to impose negligible load on the host. Here, we characterised a library of aptamers when expressed from different promoters in two Escherichia coli strains. We found that aptamer performance is dependent on the context of expression, and that, contrary to expectation, aptamer production impacts host fitness. We then built a library of burden-responsive biosensors testing their response to heterologous expression. The tRNA-Broc biosensor was selected for its fluorescence response, minimal impact on growth and ability to differentiate the burden imposed by different expression levels and constructs. The biosensor developed here adds to the collection of tools available to characterise burden and support applications where improved host performance is sought.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2566-2585"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sebum analysis as an advantageous source of biomolecular information. 皮脂分析作为生物分子信息的有利来源。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-04-24 DOI: 10.1016/j.tibtech.2025.03.015
Eden Morales-Narváez
{"title":"Sebum analysis as an advantageous source of biomolecular information.","authors":"Eden Morales-Narváez","doi":"10.1016/j.tibtech.2025.03.015","DOIUrl":"10.1016/j.tibtech.2025.03.015","url":null,"abstract":"<p><p>Sebum, a valuable yet underexplored source of biomolecular information, offers non-invasive collection, but its analysis presents challenges due to its hydrophobic and viscous nature. This forum article highlights the challenges but immense potential of sebum analysis in shaping the next generation of diagnostics and other biotechnological applications.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2392-2394"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation. 恶臭假单胞菌合成丝氨酸循环的系统工程揭示了甲醇同化的新兴拓扑结构。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-07-05 DOI: 10.1016/j.tibtech.2025.06.001
Òscar Puiggené, Jaime Muñoz-Triviño, Laura Civil-Ferrer, Line Gille, Helena Schulz-Mirbach, Daniel Bergen, Tobias J Erb, Birgitta E Ebert, Pablo I Nikel
{"title":"Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation.","authors":"Òscar Puiggené, Jaime Muñoz-Triviño, Laura Civil-Ferrer, Line Gille, Helena Schulz-Mirbach, Daniel Bergen, Tobias J Erb, Birgitta E Ebert, Pablo I Nikel","doi":"10.1016/j.tibtech.2025.06.001","DOIUrl":"10.1016/j.tibtech.2025.06.001","url":null,"abstract":"<p><p>The urgent need for a circular carbon economy has driven research into sustainable substrates, including one-carbon (C<sub>1</sub>) compounds. The non-pathogenic soil bacterium Pseudomonas putida is a promising host for exploring synthetic methylotrophy due to its versatile metabolism. In this research article we implemented synthetic serine cycle variants in P. putida for methanol assimilation, combining modular engineering and growth-coupled selection, whereby methanol assimilation supported biosynthesis of the essential amino acid serine. We adopted three synthetic variants (serine-threonine cycle, homoserine cycle, and modified serine cycle), divided these metabolic architectures into functional modules, and systematically compared their performance for in vivo implementation. Additionally, we harnessed native pyrroloquinoline quinone (PQQ)-dependent dehydrogenases for engineering methylotrophy. Recursive rewiring of synthetic and native activities revealed novel metabolic topologies for methanol utilization, termed enhanced serine-threonine cycle, providing a blueprint for engineering C<sub>1</sub> assimilation in non-model heterotrophic bacteria.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2539-2565"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144567871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The metabolic guide to space survival. 太空生存的代谢指南。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-09-13 DOI: 10.1016/j.tibtech.2025.08.012
Kristina Pulejkova, Diethard Mattanovich
{"title":"The metabolic guide to space survival.","authors":"Kristina Pulejkova, Diethard Mattanovich","doi":"10.1016/j.tibtech.2025.08.012","DOIUrl":"10.1016/j.tibtech.2025.08.012","url":null,"abstract":"","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2379-2382"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145065683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scaling DNA engineering. 缩放DNA工程。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-05-28 DOI: 10.1016/j.tibtech.2025.05.002
Weiyi Li, Po-Hsiang Hung, Takeshi Matsui, Sasha F Levy, Gavin Sherlock
{"title":"Scaling DNA engineering.","authors":"Weiyi Li, Po-Hsiang Hung, Takeshi Matsui, Sasha F Levy, Gavin Sherlock","doi":"10.1016/j.tibtech.2025.05.002","DOIUrl":"10.1016/j.tibtech.2025.05.002","url":null,"abstract":"<p><p>DNA can be engineered to produce new biologics, gene therapies, and cellular therapies, and to reprogram organisms. Having the ability to engineer DNA at scale can accelerate the development of these applications. Existing technologies excel at short oligonucleotide synthesis by chemical or enzymatic methods (up to 2000 bp) and intermediate-size DNA assembly (up to 5-7 kb). Yet synthesizing sequence-validated longer DNA (>10 kb) and/or constructing highly complex combinatorial DNA libraries at scale remains a significant challenge, due largely to technical and cost barriers. Inspired by recent studies on an in vivo DNA processing platform for megabase-long DNA assembly and on high-throughput sequence verification, we discuss how these platforms may be used to achieve DNA engineering at scale.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2399-2409"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12360497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","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 homologous recombination-proficient Yarrowia lipolytica chassis for multiplex genome manipulation. 用于多重基因组操作的同源重组精通脂溶耶氏菌底盘。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-07-09 DOI: 10.1016/j.tibtech.2025.06.009
Lu Shan, Kevin J Verstrepen, Qinhong Wang, Zongjie Dai
{"title":"A homologous recombination-proficient Yarrowia lipolytica chassis for multiplex genome manipulation.","authors":"Lu Shan, Kevin J Verstrepen, Qinhong Wang, Zongjie Dai","doi":"10.1016/j.tibtech.2025.06.009","DOIUrl":"10.1016/j.tibtech.2025.06.009","url":null,"abstract":"<p><p>Homologous recombination (HR) greatly facilitates precise genome editing. However, most organisms prefer error-prone non-homologous end joining (NHEJ) for DNA double-strand break (DSB) repair. Here, the NHEJ-proficient Yarrowia lipolytica was transformed into a HR-proficient strain by systematic engineering of recombination machinery, regulating the multiinvasion-induced rearrangement (MIR) process, and expressing cognate single-stranded DNA-annealing protein (SSAP)-single-stranded DNA-binding protein (SSB) pairs. These strategies improved HR efficiency by 38.9, 1.6, and 1.2-fold compared with the NHEJ-deficient strain for multifragment multisite integration, and multi- and single-fragment single-site integration, respectively. Moreover, HR efficiency remained high at 58% even with 50-base pair (bp) homology arms (HAs) and reached 11% for simultaneously integrating two mega-DNA fragments (18.0 kb and 13.5 kb) at two genome sites. This strain also enabled simultaneous editing, repression, and activation of multiple genes, while cellular robustness parameters showed marked increases over the NHEJ-deficient strain. Our work provides a HR-proficient Y. lipolytica chassis allowing efficient and precise genome editing of this increasingly important microbe.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2627-2645"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Making cow-free caseins and casein micelles. 制造不含奶牛的酪蛋白和酪蛋白胶束。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-09-08 DOI: 10.1016/j.tibtech.2025.08.016
Carl Holt
{"title":"Making cow-free caseins and casein micelles.","authors":"Carl Holt","doi":"10.1016/j.tibtech.2025.08.016","DOIUrl":"10.1016/j.tibtech.2025.08.016","url":null,"abstract":"<p><p>A key step in the precision fermentation of casein proteins is correct phosphorylation to generate one or more short linear sequence motifs (SLiMs) containing three or more phosphorylated seryl residues. The work of Balasubramanian et al. takes us a step closer to that goal by showing that two bacterial phosphokinases are promising alternatives to the mammalian Golgi phosphokinases and casein kinase-II.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2389-2391"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The next Green Revolution: integrating crop architectype and physiotype. 下一次绿色革命：整合作物结构型和生理型。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-04-29 DOI: 10.1016/j.tibtech.2025.04.002
Xia Li, Chen Xie, Lin Cheng, Hongning Tong, Ralph Bock, Qian Qian, Wenbin Zhou
{"title":"The next Green Revolution: integrating crop architectype and physiotype.","authors":"Xia Li, Chen Xie, Lin Cheng, Hongning Tong, Ralph Bock, Qian Qian, Wenbin Zhou","doi":"10.1016/j.tibtech.2025.04.002","DOIUrl":"10.1016/j.tibtech.2025.04.002","url":null,"abstract":"<p><p>In the middle of the last century, the Green Revolution dramatically increased crop yields and transformed global agriculture. As current food production is increasingly challenged by the demands of the growing population, climate change, and environmental degradation, a new Green Revolution is urgently needed. This Review highlights recent progress in defining the morphological ideotypes of four major crops, and proposes essential physiological traits critical for crop improvement and environmental adaptation. We introduce two concepts: the 'architectype' representing optimized morphological features, and the 'physiotype' encompassing improved physiological traits. By integrating these concepts through advanced genomic technologies and precision management practices, the next Green Revolution could potentially enhance crop yields and resource use efficiency by over 20-30%, thereby ensuring sustainable food production.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2479-2493"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tunable dynamic engineering of cellular NAD boosts the production of antibiotics in actinomycetes. 细胞NAD的可调动态工程促进了放线菌中抗生素的产生。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-10-01 Epub Date: 2025-07-05 DOI: 10.1016/j.tibtech.2025.06.003
Panpan Wu, Zhenyue Xu, Zhongqiu Meng, Ketao Chen, Hao Lin, Min Zhang, Lixin Zhang, Buchang Zhang, Hang Wu
{"title":"Tunable dynamic engineering of cellular NAD boosts the production of antibiotics in actinomycetes.","authors":"Panpan Wu, Zhenyue Xu, Zhongqiu Meng, Ketao Chen, Hao Lin, Min Zhang, Lixin Zhang, Buchang Zhang, Hang Wu","doi":"10.1016/j.tibtech.2025.06.003","DOIUrl":"10.1016/j.tibtech.2025.06.003","url":null,"abstract":"<p><p>Nicotinamide adenine dinucleotide (NAD) homeostasis is crucial for secondary metabolism in antibiotic-producing actinomycetes. However, NAD-based dynamic control strategies for boosting antibiotic titers have not been reported. We identified SACE_1905, an alcohol dehydrogenase in Saccharopolyspora erythraea, which converts NADH to NAD<sup>+</sup>. Overexpressing SACE_1905 lowered the cellular NADH/NAD<sup>+</sup> ratio, facilitating carbon source utilization and erythromycin biosynthetic precursor supply, concurrently improving cell growth and erythromycin yield. To balance primary and secondary metabolism, we developed a strategy that fine-tunes SACE_1905 expression with inducible clustered regularly interspaced short palindromic repeat interference (CRISPRi) to dynamically modulate the NADH/NAD<sup>+</sup> ratio, which we named diNAD. Optimized diNAD redirected carbon flux, maximizing erythromycin biosynthesis at a moderate NADH/NAD<sup>+</sup> ratio during the stationary phase. Based on its utility in actinorhodin and avermectin overproduction in Streptomyces coelicolor and Streptomyces avermitilis, we show that diNAD is effective in augmenting antibiotic titers in actinomycetes.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2586-2608"},"PeriodicalIF":14.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144567872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Brown adipose tissue engineering: advances, challenges, and future directions. 褐色脂肪组织工程：进展、挑战和未来方向。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-09-25 DOI: 10.1016/j.tibtech.2025.08.010
Aslı Sena Karanfil, Fiona Louis, Michiya Matsusaki
{"title":"Brown adipose tissue engineering: advances, challenges, and future directions.","authors":"Aslı Sena Karanfil, Fiona Louis, Michiya Matsusaki","doi":"10.1016/j.tibtech.2025.08.010","DOIUrl":"https://doi.org/10.1016/j.tibtech.2025.08.010","url":null,"abstract":"<p><p>Obesity is a major health issue as it increases the risk of developing chronic diseases, including cardiovascular disorders, diabetes, and certain types of cancer. Brown adipose tissue (BAT) is a promising target for obesity treatment due to its ability to burn fat and create heat via non-shivering thermogenesis. The development of BAT models for therapeutic use has become possible through recent advances in tissue engineering, including stem cell-based methods, 3D bioprinting, and organoid systems. However, optimizing differentiation protocols while maintaining the physiological relevance of BAT remains challenging. This review explores current advances in BAT engineering and highlights future research priorities for achieving clinical applications in metabolic health interventions.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145179061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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