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Prenol production in a microbial host via the "Repass" Pathways.
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-25 DOI: 10.1016/j.ymben.2025.01.009
David N Carruthers, Isaac Donnell, Eric Sundstrom, Jay D Keasling, Taek Soon Lee
{"title":"Prenol production in a microbial host via the \"Repass\" Pathways.","authors":"David N Carruthers, Isaac Donnell, Eric Sundstrom, Jay D Keasling, Taek Soon Lee","doi":"10.1016/j.ymben.2025.01.009","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.01.009","url":null,"abstract":"<p><p>Prenol and isoprenol are promising advanced biofuels and serve as biosynthetic precursors for pharmaceuticals, fragrances, and other industrially relevant compounds. Despite engineering improvements that circumvent intermediate cytotoxicity and lower energy barriers, achieving high titer 'mevalonate (MVA)-derived' prenol has remained elusive. Difficulty in selective prenol production stems from the necessary isomerization of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMAPP) as well as the intrinsic toxicity of these diphosphate precursors. Here, the expression of specific isopentenyl monophosphate kinases with model-guided enzyme substitution of diphosphate isomerases and phosphatases enabled selective cycling of monophosphates and diphosphates, dramatically improving prenol titers and selectivity in Escherichia coli. Pairing this approach with the canonical MVA pathway resulted in 300 mg/L prenol at a 30:1 ratio with isoprenol. Further pairing with the \"IPP-Bypass\" pathway resulted in 526 mg/L prenol at a 72:1 ratio with isoprenol, the highest and purest MVA-derived prenol titer to date. Additionally, modifying this \"IPP-Repass\" for DMAPP production and coexpressing the prenyltransferase acPT1 yielded 48.3 mg/L of the potential therapeutic precursor drupanin from p-coumarate. These novel repass pathways establish a unique strategy for tuning diphosphate precursors to drive isoprenoid biosynthesis and prenylation reactions.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052494","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}
引用次数: 0
Exploring and increased acetate biosynthesis in Synechocystis PCC 6803 through insertion of a heterologous phosphoketolase and overexpressing phosphotransacetylase.
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-23 DOI: 10.1016/j.ymben.2025.01.008
Stamatina Roussou, Minmin Pan, Jens Krömer, Peter Lindblad
{"title":"Exploring and increased acetate biosynthesis in Synechocystis PCC 6803 through insertion of a heterologous phosphoketolase and overexpressing phosphotransacetylase.","authors":"Stamatina Roussou, Minmin Pan, Jens Krömer, Peter Lindblad","doi":"10.1016/j.ymben.2025.01.008","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.01.008","url":null,"abstract":"<p><p>Acetate is a biological anion with many applications in the chemical and food industries. In addition to being a common microbial fermentative end-product, acetate can be produced by photosynthetic cyanobacteria from CO<sub>2</sub> using solar energy. Using wild-type cells of the unicellular model cyanobacterium Synechocystis PCC 6803 only low levels of acetate are observed outside the cells. By inserting a heterologous phosphoketolase (PKPa) in the acs locus, encoding acetyl-CoA synthetase responsible for the irreversible conversion of acetate to acetyl-CoA, an increased level of 40 times was observed. Metabolite analyses indicate an enhanced Calvin-Benson-Bassham cycle, based on increased levels of glyceraldehyde 3-phosphate and fructose-1,6-biphosphate, while the decreased levels of 3-phosphoglycerate and pyruvate suggest a quick consumption of the fixed carbon. Acetyl-P and erythrose-4-phosphate showed significantly increased levels, as products of phosphoketolase, while acetyl-CoA remained stable through the experiment. The results of intra- and extra-cellular acetate levels clearly demonstrate an efficient excretion of produced acetate from the cells in the engineered strain. Knock-out of ach and pta showed a reduction in acetate production however, it was not as low as in cells with a single knock-out of ach. Overexpressing acetyl-CoA hydrolase (Ach) and acetate kinase (AckA) did not significantly increase production. In contrast, overexpressing phosphotransacetylase (Pta) in cells containing an inserted PKPa resulted in 80 times more acetate reaching 2.3 g/L after 14 days of cultivation.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143039921","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}
引用次数: 0
Introduction of acetyl-phosphate bypass and increased culture temperatures enhanced growth-coupled poly-hydroxybutyrate production in the marine cyanobacterium Synechococcus sp. PCC7002.
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-21 DOI: 10.1016/j.ymben.2025.01.004
Kosuke Inabe, Ryota Hidese, Yuichi Kato, Mami Matsuda, Takanobu Yoshida, Keiji Matsumoto, Akihiko Kondo, Shunsuke Sato, Tomohisa Hasunuma
{"title":"Introduction of acetyl-phosphate bypass and increased culture temperatures enhanced growth-coupled poly-hydroxybutyrate production in the marine cyanobacterium Synechococcus sp. PCC7002.","authors":"Kosuke Inabe, Ryota Hidese, Yuichi Kato, Mami Matsuda, Takanobu Yoshida, Keiji Matsumoto, Akihiko Kondo, Shunsuke Sato, Tomohisa Hasunuma","doi":"10.1016/j.ymben.2025.01.004","DOIUrl":"10.1016/j.ymben.2025.01.004","url":null,"abstract":"<p><p>Polyhydroxyalkanoate (PHA) is an attractive bio-degradable plastic alternative to petrochemical plastics. Photosynthetic cyanobacteria accumulate biomass by fixing atmospheric CO<sub>2</sub>, making them promising hosts for sustainable PHA production. Conventional PHA production in cyanobacteria requires prolonged cultivation under nutrient limitation to accumulate cellular PHA. In this study, we developed a system for growth-coupled production of the PHA poly-hydroxybutyrate (PHB), using the marine cyanobacterium Synechococcus sp. PCC 7002. A recombinant strain termed KB1 expressing a set of heterologous PHB biosynthesis genes (phaA/phaB from Cupriavidus necator H16 and phaE/phaC from Synechocystis sp. PCC 6803) accumulated substantial PHB during growth (11.4% of dry cell weight). To improve PHB accumulation, we introduced the Pseudomonas aeruginosa phosphoketolase gene (pk) into strain KB1, rewiring intermediates of the Calvin-Benson-Bassham (CBB) cycle (xyluose-5-phosphate, sedoheptulose 7-phosphate, and fructose-6-phosphate) to acetyl-CoA. The pk-expressing strain, KB15, accumulated 2.1-fold enhanced levels of PHB (23.8% of dried cell weight), relative to the parent strain, KB1. The highest PHB titer of KB15 strain supplemented with acetate was about 1.1 g L<sup>-1</sup> and the yield was further enhanced by 2.6-fold following growth at 38 °C (0.21 g L<sup>-1</sup> d<sup>-1</sup>), relative to growth at 30 °C. Metabolome analysis revealed that pool sizes of CBB intermediates decreased, while levels of acetyl-CoA increased in strain KB15 compared with strain KB1, and this increase was further enhanced following growth at 38 °C. Our data demonstrate that acetyl-phosphate generated by Pk was converted into acetyl-CoA via acetate by hitherto unidentified enzymes. In conclusion, expression of heterologous PHB biosynthesis genes enabled growth-coupled PHB production in strain PCC 7002, which was increased through acetyl-CoA supplementation by bypassing acetyl-phosphate and elevating culture temperature.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":"228-239"},"PeriodicalIF":6.8,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029073","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}
引用次数: 0
Biosynthesis of 10-Hydroxy-2-Decenoic Acid in Escherichia coli.
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-20 DOI: 10.1016/j.ymben.2025.01.006
Dan He, Yan Chen, Junfeng Shen, Han Yu, Jay D Keasling, Xiaozhou Luo
{"title":"Biosynthesis of 10-Hydroxy-2-Decenoic Acid in Escherichia coli.","authors":"Dan He, Yan Chen, Junfeng Shen, Han Yu, Jay D Keasling, Xiaozhou Luo","doi":"10.1016/j.ymben.2025.01.006","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.01.006","url":null,"abstract":"<p><p>10-hydroxy-2-decenoic acid (10-HDA), a unique unsaturated fatty acid present in royal jelly, has attracted considerable interest due to its potential medical applications. However, its low concentration in royal jelly and complex conformational structure present challenges for large-scale production. In this study, we designed and constructed a de novo biosynthetic pathway for 10-HDA in Escherichia coli. Initially, we introduced the heterologous thioesterase UaFatB1 to hydrolyze trans-2-decenoyl ACP to produce trans-2-decenoic acid, a key precursor for 10-HDA. Subsequently, we employed the bacterial cytochrome P450 enzyme CYP153AMaq to catalyze the terminal hydroxylation of trans-2-decenoic acid. Furthermore, through redox partner engineering and directed evolution, we identified the optimal combination for 10-HDA production: CYP153AMaq Q129R/V141L mutant with redox partner FdR0978/Fdx0338. Finally, we optimized the fermentation conditions and achieved a 10-HDA titer of 18.8 mg/L using glucose as primary carbon source. Our work establishes a platform for producing α,β-unsaturated fatty acids and its derivatives, facilitating more study of these compounds.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":""},"PeriodicalIF":6.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143023877","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}
引用次数: 0
Unleashing the innate ability of Escherichia coli to produce D-Allose. 释放大肠杆菌产生D-Allose的先天能力。
IF 8.4 1区 生物学
Metabolic engineering Pub Date : 2025-01-18 DOI: 10.1016/j.ymben.2025.01.007
Bryant Luu,Dileep Sai Kumar Palur,Jayce E Taylor,John Didzbalis,Justin B Siegel,Shota Atsumi
{"title":"Unleashing the innate ability of Escherichia coli to produce D-Allose.","authors":"Bryant Luu,Dileep Sai Kumar Palur,Jayce E Taylor,John Didzbalis,Justin B Siegel,Shota Atsumi","doi":"10.1016/j.ymben.2025.01.007","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.01.007","url":null,"abstract":"D-allose is a rare monosaccharide, found naturally in low abundances. Due to its low-calorie profile and similar taste to sucrose, D-allose has the potential to become an ideal sugar substitute. D-allose also displays unique properties and health benefits that can be applied to various fields, including food and medicine. D-allose can be produced using two enzymatic steps in vitro: the epimerization of D-fructose, then the isomerization of the resulting D-psicose. This method suffers from poor yield due to the reversible nature of both reactions. We found that Escherichia coli possesses all of the required enzymes to convert D-glucose to D-allose with a thermodynamically favorable pathway, through a series of phosphorylation-epimerization-isomerization-dephosphorylation steps. To increase carbon flux toward D-allose production, the pathway genes were additionally expressed, and the competing pathways were removed. The engineered strains achieved production of D-allose, at a titer of 56.4 g L-1, a productivity of 0.65 g L-1 hr1, and a yield of 41.4% under test tube conditions.","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"32 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142991832","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}
引用次数: 0
Designing a microbial factory suited for plant chloroplast-derived enzymes to efficiently and green synthesize natural products: capsanthin and capsorubin as examples. 设计一种适合植物叶绿体衍生酶的微生物工厂,以高效、绿色地合成天然产物:辣椒素和辣椒素。
IF 8.4 1区 生物学
Metabolic engineering Pub Date : 2025-01-16 DOI: 10.1016/j.ymben.2025.01.005
Huibin Chen,Guiping Guo,Qiaoyue Li,Zhen Liu
{"title":"Designing a microbial factory suited for plant chloroplast-derived enzymes to efficiently and green synthesize natural products: capsanthin and capsorubin as examples.","authors":"Huibin Chen,Guiping Guo,Qiaoyue Li,Zhen Liu","doi":"10.1016/j.ymben.2025.01.005","DOIUrl":"https://doi.org/10.1016/j.ymben.2025.01.005","url":null,"abstract":"Specific cellular microenvironment, multi-enzyme complex and expensive essential cofactor make the biological manufacturing of plant chloroplast natural products (PCNPs) extremely challenging. The above difficulties have hampered the biosynthesis of capsanthin and capsorubin in the past 30 years. Here, we take capsanthin and capsorubin as examples to design an innovative microbial factory to promote the heterologous synthesis of PCPNs. Our main strategy is mimicking the microenvironment of chloroplasts in microbial factory. First, accumulation of violaxanthin, which is the key precursor, was increased by 587.9%, through introducing oxidative microenvironment and thioredoxin. The initial capsanthin-producing strain with 0.28 mg g-1 DCW were obtained by introducing capsanthin/capsorubin synthase (CCS). Subsequently, chloroplast-derived chaperones Cpn60α, Cpn60β and Cpn20 created a folding-promoting microenvironment for CCS. At the same time, by imitating the quasi-natural CCS, an artificial homotrimer was constructed and obtained 5.15 mg g-1 DCW capsanthin, and 1.62 mg g-1 DCW capsorubin. Finally, sufficient FADH2 was provided for CCS by feeding 20 mM formate. This process was realized by the continuous catalysis of formate dehydrogenase and flavin reductase. The engineered strain accumulated 6.77 mg g-1 DCW of capsanthin and 2.18 mg g-1 DCW of capsorubin. Compared with the initial strain, the yield of capsanthin was increased by 24.18 times, and 13.54 times of the highest yield reported so far. Artificially designed microbial cell factory and low-cost cofactor supply methods are in line with the current sustainable and green wave of biochemicals. This work not only provides a platform strain for low-cost and sustainable biosynthesis, but also provides a paradigm for heterologous expression of chloroplast-derived enzymes.","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"20 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142991745","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}
引用次数: 0
De novo biosynthesis of mogroside V by multiplexed engineered yeasts. 多重工程酵母重新合成甜苷V的研究。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-07 DOI: 10.1016/j.ymben.2025.01.002
Guanyi Qu, Yunfei Song, Xianhao Xu, Yanfeng Liu, Jianghua Li, Guocheng Du, Long Liu, Yangyang Li, Xueqin Lv
{"title":"De novo biosynthesis of mogroside V by multiplexed engineered yeasts.","authors":"Guanyi Qu, Yunfei Song, Xianhao Xu, Yanfeng Liu, Jianghua Li, Guocheng Du, Long Liu, Yangyang Li, Xueqin Lv","doi":"10.1016/j.ymben.2025.01.002","DOIUrl":"10.1016/j.ymben.2025.01.002","url":null,"abstract":"<p><p>High sugar intake has become a global health concern due to its association with various diseases. Mogroside V (MG-V), a zero-calorie sweetener with multiple medical properties, is emerging as a promising sugar substitute. However, its application is hindered by low natural abundance and the inefficiency of conventional plant extraction methods. In this study, two glycosyltransferases were introduced into an engineered mogrol-producing Saccharomyces cerevisiae strain to enable the first de novo MG-V biosynthesis. Then, MG-V titer increased by 2.3 × 10<sup>4</sup>-fold through a series of efficient metabolic engineering strategies, including the enhancement of precursors, inhibition of the competitive pathway, and prevention of MG-V degradation. The challenges of enzyme spatial separation and high protein folding stress were addressed through lipid droplet (LD) compartmentalization and endoplasmic reticulum expansion, respectively. The ty1 transposon was employed to increase the copies of LD-targeted fusion protein AtCPR2-CYP87D18, which possessed higher CYP450 catalytic efficiency, resulting in an MG-V titer of 10.25 mg/L in shake flasks and 28.62 mg/L in a 5-L bioreactor. Overall, this study realized de novo MG-V synthesis in S. cerevisiae for the first time and provided a valuable reference for constructing microbial factories for triterpenoid saponin synthesis.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":"160-171"},"PeriodicalIF":6.8,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951316","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}
引用次数: 0
CIFR (Clone-Integrate-Flip-out-Repeat): A toolset for iterative genome and pathway engineering of Gram-negative bacteria. CIFR(克隆-整合-翻转-重复):革兰氏阴性菌迭代基因组和途径工程的工具集。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-06 DOI: 10.1016/j.ymben.2025.01.001
Filippo Federici, Francesco Luppino, Clara Aguilar-Vilar, Maria Eleni Mazaraki, Lars Boje Petersen, Linda Ahonen, Pablo I Nikel
{"title":"CIFR (Clone-Integrate-Flip-out-Repeat): A toolset for iterative genome and pathway engineering of Gram-negative bacteria.","authors":"Filippo Federici, Francesco Luppino, Clara Aguilar-Vilar, Maria Eleni Mazaraki, Lars Boje Petersen, Linda Ahonen, Pablo I Nikel","doi":"10.1016/j.ymben.2025.01.001","DOIUrl":"10.1016/j.ymben.2025.01.001","url":null,"abstract":"<p><p>Advanced genome engineering enables precise and customizable modifications of bacterial species, and toolsets that exhibit broad-host compatibility are particularly valued owing to their portability. Tn5 transposon vectors have been widely used to establish random integrations of desired DNA sequences into bacterial genomes. However, the iteration of the procedure remains challenging because of the limited availability and reusability of selection markers. We addressed this challenge with CIFR, a mini-Tn5 integration system tailored for iterative genome engineering. The pCIFR vectors incorporate attP and attB sites flanking an antibiotic resistance marker used to select for the insertion. Subsequent removal of antibiotic determinants is facilitated by the Bxb1 integrase paired to a user-friendly counter-selection marker, both encoded in auxiliary plasmids. CIFR delivers engineered strains harboring stable DNA insertions and free of any antibiotic resistance cassette, allowing for the reusability of the tool. The system was validated in Pseudomonas putida, Escherichia coli, and Cupriavidus necator, underscoring its portability across diverse industrially relevant hosts. The CIFR toolbox was calibrated through combinatorial integrations of chromoprotein genes in P. putida, generating strains displaying a diverse color palette. We also introduced a carotenoid biosynthesis pathway in P. putida in a two-step engineering process, showcasing the potential of the tool for pathway balancing. The broad utility of the CIFR toolbox expands the toolkit for metabolic engineering, allowing for the construction of complex phenotypes while opening new possibilities in bacterial genetic manipulations.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":"180-195"},"PeriodicalIF":6.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951312","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}
引用次数: 0
Cross-feeding of amino acid pathway intermediates is common in co-cultures of auxotrophic Escherichia coli. 氨基酸途径中间体的交叉饲养在营养不良的大肠杆菌共培养中很常见。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-06 DOI: 10.1016/j.ymben.2025.01.003
Yu-Jun Hong, Yijing Cai, Maciek R Antoniewicz
{"title":"Cross-feeding of amino acid pathway intermediates is common in co-cultures of auxotrophic Escherichia coli.","authors":"Yu-Jun Hong, Yijing Cai, Maciek R Antoniewicz","doi":"10.1016/j.ymben.2025.01.003","DOIUrl":"10.1016/j.ymben.2025.01.003","url":null,"abstract":"<p><p>Amino acid auxotrophy refers to an organism's inability to synthesize one or more amino acids that are required for cell growth. In microbiome research, co-cultures of amino acid auxotrophs are often used to investigate metabolite cross-feeding interactions and model community dynamics. Thus far, it has been implicitly assumed that amino acids are mainly cross-fed between these auxotrophs. However, this assumption has not been fully verified. For example, it could be that intermediates of amino acid biosynthesis pathways are exchanged instead, or in addition to amino acids. If true, this would significantly increase the complexity of metabolic interactions that needs to be considered. Here, we show that metabolic pathway intermediates are indeed exchanged in many co-cultures of amino acid auxotrophs. To demonstrate this, we selected 25 E. coli single gene knockouts that are auxotrophic for five different amino acids: arginine, histidine, isoleucine, proline, and tryptophan. In co-culture experiments, we paired strains that shared the same amino acid auxotrophy and monitored cell growth. We observed growth in 23 out of 55 strain pairings, indicating that pathway intermediates were exchanged between the strains. To provide further support for cross-feeding of pathway intermediates, auxotrophic E. coli strains were cultured in media supplemented with commercially available metabolic pathway intermediates at different concentrations. Supplementing media with these metabolites recovered cell growth as was predicted from the co-culture experiments. Most of these metabolites supported high growth rates, even when present at low concentrations (10 μM), suggesting the presence of high affinity transporters for these metabolites. In total, we identified eight metabolic pathway intermediates that were likely exchanged between the auxotrophic E. coli strains and verified six of these, including histidinol, N-acetyl-L-ornithine, L-ornithine, L-citrulline, keto-isoleucine and anthranilate. Taken together, this work demonstrates that exchange of metabolic pathway intermediates is more common than has been assumed so far. In future, these exchanges must be explicitly considered when constructing models of metabolite cross-feeding interactions in microbial communities and when interpreting results from microbiome studies involving auxotrophic strains.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":"172-179"},"PeriodicalIF":6.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951314","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}
引用次数: 0
Deep learning for NAD/NADP cofactor prediction and engineering using transformer attention analysis in enzymes. 利用深度学习对酶中的转化注意分析进行 NAD/NADP 辅因子预测和工程设计。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-01-01 Epub Date: 2024-11-20 DOI: 10.1016/j.ymben.2024.11.007
Jaehyung Kim, Jihoon Woo, Joon Young Park, Kyung-Jin Kim, Donghyuk Kim
{"title":"Deep learning for NAD/NADP cofactor prediction and engineering using transformer attention analysis in enzymes.","authors":"Jaehyung Kim, Jihoon Woo, Joon Young Park, Kyung-Jin Kim, Donghyuk Kim","doi":"10.1016/j.ymben.2024.11.007","DOIUrl":"10.1016/j.ymben.2024.11.007","url":null,"abstract":"<p><p>Understanding and manipulating the cofactor preferences of NAD(P)-dependent oxidoreductases, the most widely distributed enzyme group in nature, is increasingly crucial in bioengineering. However, large-scale identification of the cofactor preferences and the design of mutants to switch cofactor specificity remain as complex tasks. Here, we introduce DISCODE (Deep learning-based Iterative pipeline to analyze Specificity of COfactors and to Design Enzyme), a novel transformer-based deep learning model to predict NAD(P) cofactor preferences. For model training, a total of 7,132 NAD(P)-dependent enzyme sequences were collected. Leveraging whole-length sequence information, DISCODE classifies the cofactor preferences of NAD(P)-dependent oxidoreductase protein sequences without structural or taxonomic limitation. The model showed 97.4% and 97.3% of accuracy and F1 score, respectively. A notable feature of DISCODE is the interpretability of its transformer layers. Analysis of attention layers in the model enables identification of several residues that showed significantly higher attention weights. They were well aligned with structurally important residues that closely interact with NAD(P), facilitating the identification of key residues for determining cofactor specificities. These key residues showed high consistency with verified cofactor switching mutants. Integrated into an enzyme design pipeline, DISCODE coupled with attention analysis, enables a fully automated approach to redesign cofactor specificity.</p>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":" ","pages":"86-94"},"PeriodicalIF":6.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687367","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}
引用次数: 0
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