Wei Jiang, William Newell, Jingjing Liu, Lucas Coppens, Khushboo Borah Slater, Huadong Peng, David Bell, Long Liu, Victoria Haritos, Rodrigo Ledesma-Amaro
{"title":"Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering.","authors":"Wei Jiang, William Newell, Jingjing Liu, Lucas Coppens, Khushboo Borah Slater, Huadong Peng, David Bell, Long Liu, Victoria Haritos, Rodrigo Ledesma-Amaro","doi":"10.1016/j.ymben.2025.03.014","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.03.014","url":null,"abstract":"<p><p>Methanol is a promising sustainable alternative feedstock for green biomanufacturing. The yeast Yarrowia lipolytica offers a versatile platform for producing a wide range of products but it cannot use methanol efficiently. In this study, we engineered Y. lipolytica to utilize methanol by overexpressing a methanol dehydrogenase, followed by the incorporation of methanol assimilation pathways from methylotrophic yeasts and bacteria. We also overexpressed the ribulose monophosphate (RuMP) and xylulose monophosphate (XuMP) pathways, which led to significant improvements in growth with methanol, reaching a consumption rate of 2.35 g/L in 24 hours and a 2.68-fold increase in biomass formation. Metabolomics and Metabolite Flux Analysis confirmed methanol assimilation and revealed an increase in reducing power. The strains were further engineered to produce the valuable heterologous product resveratrol from methanol as a co-substrate. Unlike traditional methanol utilization processes, which are often resource-intensive and environmentally damaging, our findings represent a significant advance in green chemistry by demonstrating the potential of Y. lipolytica for efficient use of methanol as a co-substrate for energy, biomass, and product formation. This work not only contributes to our understanding of methanol metabolism in non-methylotrophic organisms but also paves the way for achieving efficient synthetic methylotrophy towards green biomanufacturing.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"BGC heteroexpression strategy for production of novel microbial secondary metabolites.","authors":"Yuanyuan Liu, Yuqi Tang, Zhiyang Fu, Wangjie Zhu, Hong Wang, Huawei Zhang","doi":"10.1016/j.ymben.2025.03.018","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.03.018","url":null,"abstract":"<p><p>Biosynthetic gene clusters (BGCs) in microbial genomes play a crucial role in the biosynthesis of diverse secondary metabolites (SMs) with pharmaceutical potential. However, most BGCs remain silent under conventional conditions, resulting in the frequently repeated discovery of known SMs. Fortunately, in the past two decades, the heterologous expression of BGCs in genetically tractable hosts has emerged as a powerful strategy to awaken microbial metabolic pathways for making novel microbial SMs. In this review, we comprehensively delineated the development and application of this strategy, highlighting various BGC cloning and assembly techniques and their technical characteristics. We also summarized 519 novel SMs from BGC hetero-expression-derived strains and described their occurrence, bioactivity, mode of action, and biosynthetic logic. Lastly, current challenges and future perspectives for developing more efficient BGC hetero-expression strategies were discussed in this review.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rongsheng Li, Shuang Guo, Dong Wang, Tingting Yang, Wenhao Li, Jie Wang, Luqi Huang, Xueli Zhang, Zhubo Dai
{"title":"Elucidation of the plant progesterone biosynthetic pathway and its application in a yeast cell factory.","authors":"Rongsheng Li, Shuang Guo, Dong Wang, Tingting Yang, Wenhao Li, Jie Wang, Luqi Huang, Xueli Zhang, Zhubo Dai","doi":"10.1016/j.ymben.2025.03.016","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.03.016","url":null,"abstract":"<p><p>Progesterone and its steroidal derivatives, including androgens, estrogens, glucocorticoids and mineralocorticoids are extensively utilized in pharmacotherapy, serving as predominant agents in anti-inflammatory, contraceptive, and anticancer treatments. From the 1990s to the present, scientists attempted to biosynthesize steroids such as progesterone and hydrocortisone from sugars in engineered microbial strains expressing pathway enzymes derived from animal sources. However, the low activity of the cytochrome P450 sterol side-chain cleavage (P450scc) system and their mitochondrial compartmentalization have limited the development of this route. Therefore, discovering an efficient P450scc system and developing innovative strategies will be necessary to overcome this bottleneck. Here, we elucidated the complete biosynthetic pathway of progesterone in Marsdenia tenacissima, a medicinal plant rich in steroids. The pathway comprises four enzymes, the two P450scc enzymes MtCYP108 and MtCYP150, as well as the two 3β-hydroxysteroid dehydrogenase/Δ<sup>5</sup>-Δ<sup>4</sup> isomerases MtHSD5 and MtHSD6. Unlike their animal counterparts, the plant-derived P450scc were found to be localized to the endoplasmic reticulum in yeast and plants, and using the plant-type cytochrome P450 reductase (CPR) as electron transfer chain. The plant-derived HSDs are cytoplasmic in yeast and plants, whereas animal-derived HSDs localize to the endoplasmic reticulum. According to this discovery, we engineered a yeast-based cell factory capable of synthesizing 1.06 g/L of progesterone from a simple carbon source. This discovery lays the groundwork for the sustainable synthesis of steroid hormone drugs through the use of plant-based systems or microbial host cells.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Rhodotorula sp. as a promising host for microbial cell factories","authors":"Baisong Tong, Yi Yu, Shuobo Shi","doi":"10.1016/j.ymben.2025.03.015","DOIUrl":"10.1016/j.ymben.2025.03.015","url":null,"abstract":"<div><div><em>Rhodotorula</em> sp. is a red yeast that has emerged as a promising host for microbial cell factories. Under specific conditions, <em>Rhodotorula</em> sp. can accumulate lipids that constitute over 70% of its dry cell weight, underscoring its potential in lipid compound production. Additionally, it can utilize a variety of carbon sources, including glucose, xylose, and volatile fatty acids, and exhibits high tolerance to low-cost carbon sources and industrial by-products, showcasing its excellent performance in industrial processes. Furthermore, the native mevalonate pathway of <em>Rhodotorula</em> sp. enables its efficient synthesis of antioxidant carotenoids and other terpenoids, which are widely applied in the food, pharmaceutical, and cosmetic industries. Due to its excellent accumulation ability of lipophilic compounds, metabolic diversity, and environmental adaptability, this review summarizes recent advances in genetic elements and metabolic engineering technologies for <em>Rhodotorula</em> sp., emphasizing its potential as a chassis cell factory for the production of lipids, carotenoids, and other chemicals. It also highlights key factors influencing commercial fermentation processes and concludes with challenges and solutions for further developing <em>Rhodotorula</em> sp. as microbial chassis.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 178-196"},"PeriodicalIF":6.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Engineering Komagataella phaffii to produce lycopene sustainably from glucose or methanol","authors":"Wei Zhou, Rui-Jing Ling, Yi-Chen Yang, Shu-Ting Hou, Feng-Qing Wang, Bei Gao, Dong-Zhi Wei","doi":"10.1016/j.ymben.2025.03.013","DOIUrl":"10.1016/j.ymben.2025.03.013","url":null,"abstract":"<div><div>Lycopene, a potent carotenoid with high antioxidant capacity and extensive applications, holds significant potential for sustainable production via microbial engineering, particularly with the rising interest in methanol as an ideal non-grain feedstock for a carbon-negative economy. In this study, <em>Komagataella phaffii</em> was systematically engineered to enhance lycopene production using glucose and renewable methanol as alternative carbon sources. Firstly, we demonstrated that the cytoplasmic FPP could penetrate into the peroxisome, and thus achieved the dual-localized lycopene synthesis. Subsequently, the cytoplasmic FPP pool was expanded by dynamically regulating squalene synthase and enhancing the mevalonate pathway, and FPP was redirected to lycopene synthesis via assembling critical enzymes. Furthermore, the synthesis of lycopene from methanol was improved by reprogramming the methanol metabolic pathway. In the above process, we found that the engineered strains would degrade significantly in the process of passing culture. Comparative transcriptomic analysis revealed that nitrogen metabolism genes contributed significantly to strain degeneration, and a gene (PAS_chr2-2_0003) that positively influenced lycopene synthesis was identified. Finally, two strains were successfully engineered: strain zw327, which produced 8.4 g/L lycopene from glucose, and strain zw352, which achieved 10.2 g/L from methanol and glycerol. The latter represents the highest reported titer from methanol to date, underscoring the potential of <em>K. phaffii</em> as a robust one-carbon platform for industrial terpenoid biosynthesis.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 141-153"},"PeriodicalIF":6.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Boncheol Gu, Duck Gyun Kim, Yu-jin Cha, Min-Kyu Oh
{"title":"Strategic engineering for overproduction of oviedomycin, a Type II polyketide, in Escherichia coli","authors":"Boncheol Gu, Duck Gyun Kim, Yu-jin Cha, Min-Kyu Oh","doi":"10.1016/j.ymben.2025.03.012","DOIUrl":"10.1016/j.ymben.2025.03.012","url":null,"abstract":"<div><div>This study aimed to develop a metabolically engineered <em>Escherichia coli</em> strain capable of producing oviedomycin, a type II angucyclinone polyketide compound with anticancer activity. We first addressed the challenges of <em>in vivo</em> reassembly of the type II polyketide synthase machinery in <em>E. coli</em>. These included co-expressing molecular chaperones, rare tRNAs, and a fusion tag to enhance the solubility of all proteins from the oviedomycin biosynthetic gene cluster in <em>Streptomyces antibioticus</em>. After the soluble expression of all the proteins was confirmed, oviedomycin production was improved by reducing the accumulation of the intermediate 3-dehydrorabelomycin through substrate channeling using the CipB scaffold protein from <em>Photorhabdus luminescens</em>. In addition, the AcrAB-TolC efflux transporter system was introduced to enhance the growth of the producing strain, leading to higher oviedomycin yields. Ultimately, fed-batch fermentation with the final strain produced 120 mg/L oviedomycin from glucose within 24 h. These strategies have marked significant progress in the construction of biosynthetic pathways for the heterologous production of type II polyketides in <em>E. coli</em>, offering promising potential for producing various natural products with industrial applications.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 154-164"},"PeriodicalIF":6.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
James Morrissey, Gianmarco Barberi, Benjamin Strain, Pierantonio Facco, Cleo Kontoravdi
{"title":"NEXT-FBA: A hybrid stoichiometric/data-driven approach to improve intracellular flux predictions.","authors":"James Morrissey, Gianmarco Barberi, Benjamin Strain, Pierantonio Facco, Cleo Kontoravdi","doi":"10.1016/j.ymben.2025.03.010","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.03.010","url":null,"abstract":"<p><p>Genome-scale metabolic models (GEMs) have been widely utilized to understand cellular metabolism. The application of GEMs has been advanced by computational methods that enable the prediction and analysis of intracellular metabolic states. However, the accuracy and biological relevance of these predictions often suffer from the many degrees of freedom and scarcity of available data to constrain the models adequately. Here, we introduce NEXT-FBA (Neural-net EXtracellular Trained Flux Balance Analysis), a novel computational methodology that addresses these limitations by utilizing exometabolomic data to derive biologically relevant constraints for intracellular fluxes in GEMs. We achieve this by training artificial neural networks (ANNs) with exometabolomic data from Chinese hamster ovary (CHO) cells and correlating it with <sup>13</sup>C-labeled intracellular fluxomic data. By capturing the underlying relationships between exometabolomics and cell metabolism, NEXT-FBA predicts upper and lower bounds for intracellular reaction fluxes to constrain GEMs. We demonstrate the efficacy of NEXT-FBA across several validation experiments, where it outperforms existing methods in predicting intracellular flux distributions that align closely with experimental observations. Furthermore, a case study demonstrates how NEXT-FBA can guide bioprocess optimization by identifying key metabolic shifts and refining flux predictions to yield actionable process and metabolic engineering targets. Overall, NEXT-FBA aims to improve the accuracy and biological relevance of intracellular flux predictions in metabolic modelling for bioprocess optimization, with minimal input data requirements for pre-trained models.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christos Batianis , Rik P. van Rosmalen , Pedro Moñino Fernández , Konstantinos Labanaris , Enrique Asin-Garcia , Maria Martin-Pascual , Markus Jeschek , Ruud A. Weusthuis , Maria Suarez-Diez , Vitor A.P. Martins dos Santos
{"title":"Computer-assisted multilevel optimization of malonyl-CoA availability in Pseudomonas putida","authors":"Christos Batianis , Rik P. van Rosmalen , Pedro Moñino Fernández , Konstantinos Labanaris , Enrique Asin-Garcia , Maria Martin-Pascual , Markus Jeschek , Ruud A. Weusthuis , Maria Suarez-Diez , Vitor A.P. Martins dos Santos","doi":"10.1016/j.ymben.2025.03.008","DOIUrl":"10.1016/j.ymben.2025.03.008","url":null,"abstract":"<div><div>Malonyl-CoA is the major precursor for the biosynthesis of diverse industrially valuable products such as fatty acids/alcohols, flavonoids, and polyketides. However, its intracellular availability is limited in most microbial hosts, hampering the industrial production of such chemicals. To address this limitation, we present a multilevel optimization workflow using modern metabolic engineering technologies to systematically increase the malonyl-CoA levels in <em>Pseudomonas putida</em>. The workflow involves the identification of gene downregulations, chassis selection, and optimization of the acetyl-CoA carboxylase complex through ribosome binding site engineering. Computational tools and high-throughput screening with a malonyl-CoA biosensor enabled the rapid evaluation of numerous genetic targets. Combining the most beneficial targets led to a 5.8-fold enhancement in the production titer of the valuable polyketide phloroglucinol. This study demonstrates the effective integration of computational and genetic technologies for engineering <em>P. putida</em>, opening new avenues for the development of industrially relevant strains and the investigation of fundamental biological questions.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 165-177"},"PeriodicalIF":6.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shan Yuan , Chao Xu , Miaomiao Jin , Xinglin Jiang , Wei Liu , Mo Xian , Ping Jin
{"title":"Stress-driven dynamic regulation of multiple genes to reduce accumulation of toxic aldehydes","authors":"Shan Yuan , Chao Xu , Miaomiao Jin , Xinglin Jiang , Wei Liu , Mo Xian , Ping Jin","doi":"10.1016/j.ymben.2025.03.009","DOIUrl":"10.1016/j.ymben.2025.03.009","url":null,"abstract":"<div><div>Aldehydes are ubiquitous metabolites in living cells. As reactive electrophiles, they have the capacity to form adducts with cellular protein thiols and amines, leading to potential toxicity. Dynamic regulation has proven to be an effective strategy for addressing the accumulation of toxic metabolites. However, there are limited reports on applying dynamic control specifically to mitigate aldehyde accumulation. In this study, the cinnamaldehyde accumulation in the biosynthesis of cinnamylamine was used as a model to evaluate a two-way dynamic regulation strategy. First, we utilized whole-genome transcript arrays to identify the cinnamaldehyde-responsive promoters: the upregulated promoter P<sub>4</sub> and the downregulated promoter P<sub>d</sub>. They were then employed as biosensors to dynamically regulate the synthesis and consumption of cinnamaldehyde, mitigating its toxic effects on the host. This strategy successfully reduced cinnamaldehyde accumulation by 50 % and increased the production of cinnamylamine by 2.9 times. This study demonstrated a cinnamaldehyde-induced autoregulatory system that facilitated the conversion of cinnamic acid into cinnamylamine without the need for costly external inducers, presenting a promising and economically viable approach. The strategy also serves as a reference for alleviating the inhibitory effects of other toxic aldehydes on microorganisms. Additionally, the biosensors (P<sub>d</sub> and P<sub>4</sub>) can respond to a range of aldehyde compounds, offering a rapid and sensitive method for detecting toxic aldehydes in both environmental samples and microorganisms, thus provide a valuable tool for screening strains enhanced aldehyde yield.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 129-140"},"PeriodicalIF":6.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marius Arend , Emilian Paulitz , Yunli Eric Hsieh , Zoran Nikoloski
{"title":"Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms","authors":"Marius Arend , Emilian Paulitz , Yunli Eric Hsieh , Zoran Nikoloski","doi":"10.1016/j.ymben.2025.02.015","DOIUrl":"10.1016/j.ymben.2025.02.015","url":null,"abstract":"<div><div>Advances in genomics technologies have generated large data sets that provide tremendous insights into the genetic diversity of taxonomic groups. However, it remains challenging to pinpoint the effect of genetic diversity on different traits without performing resource-intensive phenotyping experiments. Pan-genome-scale metabolic models (panGEMs) extend traditional genome-scale metabolic models by considering the entire reaction repertoire that enables the prediction and comparison of metabolic capabilities within a taxonomic group. Here, we systematically review the state-of-the-art methodologies for constructing panGEMs, focusing on used tools, databases, experimental datasets, and orthology relationships. We highlight the unique advantages of panGEMs compared to single-species GEMs in predicting metabolic phenotypes and in guiding the experimental validation of genome annotations. In addition, we emphasize the disparity between the available (pan-)genomic data on photosynthetic organisms and their under-representation in current (pan)GEMs. Finally, we propose a perspective for tackling the reconstruction of panGEMs for photosynthetic eukaryotes that can help advance our understanding of the metabolic diversity in this taxonomic group.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 67-77"},"PeriodicalIF":6.8,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}