Metabolic engineering最新文献_第7页

Engineering Escherichia coli for efficient glutathione production 改造大肠杆菌以高效生产谷胱甘肽。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2024-07-01 DOI: 10.1016/j.ymben.2024.07.001

Hiroki Mori , Misato Matsui , Takahiro Bamba , Yoshimi Hori , Sayaka Kitamura , Yoshihiro Toya , Ryota Hidese , Hisashi Yasueda , Tomohisa Hasunuma , Hiroshi Shimizu , Naoaki Taoka , Shingo Kobayashi

{"title":"Engineering Escherichia coli for efficient glutathione production","authors":"Hiroki Mori , Misato Matsui , Takahiro Bamba , Yoshimi Hori , Sayaka Kitamura , Yoshihiro Toya , Ryota Hidese , Hisashi Yasueda , Tomohisa Hasunuma , Hiroshi Shimizu , Naoaki Taoka , Shingo Kobayashi","doi":"10.1016/j.ymben.2024.07.001","DOIUrl":"10.1016/j.ymben.2024.07.001","url":null,"abstract":"<div>Glutathione is a tripeptide of excellent value in the pharmaceutical, food, and cosmetic industries that is currently produced during yeast fermentation. In this case, glutathione accumulates intracellularly, which hinders high production. Here, we engineered Escherichia coli for the efficient production of glutathione. A total of 4.3 g/L glutathione was produced by overexpressing gshA and gshB, which encode cysteine glutamate ligase and glutathione synthetase, respectively, and most of the glutathione was excreted into the culture medium. Further improvements were achieved by inhibiting degradation (Δggt and ΔpepT); deleting gor (Δgor), which encodes glutathione oxide reductase; attenuating glutathione uptake (ΔyliABCD); and enhancing cysteine production (PompF-cysE). The engineered strain KG06 produced 19.6 g/L glutathione after 48 h of fed-batch fermentation with continuous addition of ammonium sulfate as the sulfur source. We also found that continuous feeding of glycine had a crucial role for effective glutathione production. The results of metabolic flux and metabolomic analyses suggested that the conversion of O-acetylserine to cysteine is the rate-limiting step in glutathione production by KG06. The use of sodium thiosulfate largely overcame this limitation, increasing the glutathione titer to 22.0 g/L, which is, to our knowledge, the highest titer reported to date in the literature. This study is the first report of glutathione fermentation without adding cysteine in E. coli. Our findings provide a great potential of E. coli fermentation process for the industrial production of glutathione.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 180-190"},"PeriodicalIF":6.8,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538078","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

Elucidation of triacylglycerol catabolism in Yarrowia lipolytica: How cells balance acetyl-CoA and excess reducing equivalents 阐明 Yarrowia 脂溶菌中的三酰甘油分解代谢：细胞如何平衡乙酰-CoA 和过量还原当量。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2024-06-26 DOI: 10.1016/j.ymben.2024.06.010

Alyssa M. Worland , Zhenlin Han , Jessica Maruwan , Yu Wang , Zhi-Yan Du , Yinjie J. Tang , Wei Wen Su , Garrett W. Roell

{"title":"Elucidation of triacylglycerol catabolism in Yarrowia lipolytica: How cells balance acetyl-CoA and excess reducing equivalents","authors":"Alyssa M. Worland , Zhenlin Han , Jessica Maruwan , Yu Wang , Zhi-Yan Du , Yinjie J. Tang , Wei Wen Su , Garrett W. Roell","doi":"10.1016/j.ymben.2024.06.010","DOIUrl":"10.1016/j.ymben.2024.06.010","url":null,"abstract":"<div>Yarrowia lipolytica is an industrial yeast that can convert waste oil to value-added products. However, it is unclear how this yeast metabolizes lipid feedstocks, specifically triacylglycerol (TAG) substrates. This study used 13C-metabolic flux analysis (13C-MFA), genome-scale modeling, and transcriptomics analyses to investigate Y. lipolytica W29 growth with oleic acid, glycerol, and glucose. Transcriptomics data were used to guide 13C-MFA model construction and to validate the 13C-MFA results. The 13C-MFA data were then used to constrain a genome-scale model (GSM), which predicted Y. lipolytica fluxes, cofactor balance, and theoretical yields of terpene products. The three data sources provided new insights into cellular regulation during catabolism of glycerol and fatty acid components of TAG substrates, and how their consumption routes differ from glucose catabolism. We found that (1) over 80% of acetyl-CoA from oleic acid is processed through the glyoxylate shunt, a pathway that generates less CO2 compared to the TCA cycle, (2) the carnitine shuttle is a key regulator of the cytosolic acetyl-CoA pool in oleic acid and glycerol cultures, (3) the oxidative pentose phosphate pathway and mannitol cycle are key routes for NADPH generation, (4) the mannitol cycle and alternative oxidase activity help balance excess NADH generated from β-oxidation of oleic acid, and (5) asymmetrical gene expressions and GSM simulations of enzyme usage suggest an increased metabolic burden for oleic acid catabolism.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"85 ","pages":"Pages 1-13"},"PeriodicalIF":6.8,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141469294","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

A long-term growth stable Halomonas sp. deleted with multiple transposases guided by its metabolic network model Halo-ecGEM 在代谢网络模型 Halo-ecGEM 的指导下，删除了带有多种转座酶的长期生长稳定的 Halomonas sp.

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2024-06-18 DOI: 10.1016/j.ymben.2024.06.004

Lizhan Zhang , Jian-Wen Ye , Gang Li , Helen Park , Hao Luo , Yina Lin , Shaowei Li , Weinan Yang , Yuying Guan , Fuqing Wu , Wuzhe Huang , Qiong Wu , Nigel S. Scrutton , Jens Nielsen , Guo-Qiang Chen

{"title":"A long-term growth stable Halomonas sp. deleted with multiple transposases guided by its metabolic network model Halo-ecGEM","authors":"Lizhan Zhang , Jian-Wen Ye , Gang Li , Helen Park , Hao Luo , Yina Lin , Shaowei Li , Weinan Yang , Yuying Guan , Fuqing Wu , Wuzhe Huang , Qiong Wu , Nigel S. Scrutton , Jens Nielsen , Guo-Qiang Chen","doi":"10.1016/j.ymben.2024.06.004","DOIUrl":"10.1016/j.ymben.2024.06.004","url":null,"abstract":"<div>Microbial instability is a common problem during bio-production based on microbial hosts. Halomonas bluephagenesis has been developed as a chassis for next generation industrial biotechnology (NGIB) under open and unsterile conditions. However, the hidden genomic information and peculiar metabolism have significantly hampered its deep exploitation for cell-factory engineering. Based on the freshly completed genome sequence of H. bluephagenesis TD01, which reveals 1889 biological process-associated genes grouped into 84 GO-slim terms. An enzyme constrained genome-scale metabolic model Halo-ecGEM was constructed, which showed strong ability to simulate fed-batch fermentations. A visible salt-stress responsive landscape was achieved by combining GO-slim term enrichment and CVT-based omics profiling, demonstrating that cells deploy most of the protein resources by force to support the essential activity of translation and protein metabolism when exposed to salt stress. Under the guidance of Halo-ecGEM, eight transposases were deleted, leading to a significantly enhanced stability for its growth and bioproduction of various polyhydroxyalkanoates (PHA) including 3-hydroxybutyrate (3HB) homopolymer PHB, 3HB and 3-hydroxyvalerate (3HV) copolymer PHBV, as well as 3HB and 4-hydroxyvalerate (4HB) copolymer P34HB. This study sheds new light on the metabolic characteristics and stress-response landscape of H. bluephagenesis, achieving for the first time to construct a long-term growth stable chassis for industrial applications. For the first time, it was demonstrated that genome encoded transposons are the reason for microbial instability during growth in flasks and fermentors.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 95-108"},"PeriodicalIF":6.8,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432187","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

Engineering carbon source division of labor for efficient α-carotene production in Corynebacterium glutamicum 在谷氨酸棒杆菌中进行碳源分工，以高效生产 α-胡萝卜素。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2024-06-18 DOI: 10.1016/j.ymben.2024.06.008

Kai Li , Cheng Li , Chen-Guang Liu , Xin-Qing Zhao , Ruiwen Ou , Charles A. Swofford , Feng-Wu Bai , Gregory Stephanopoulos , Anthony J. Sinskey

{"title":"Engineering carbon source division of labor for efficient α-carotene production in Corynebacterium glutamicum","authors":"Kai Li , Cheng Li , Chen-Guang Liu , Xin-Qing Zhao , Ruiwen Ou , Charles A. Swofford , Feng-Wu Bai , Gregory Stephanopoulos , Anthony J. Sinskey","doi":"10.1016/j.ymben.2024.06.008","DOIUrl":"10.1016/j.ymben.2024.06.008","url":null,"abstract":"<div>Effective utilization of glucose, xylose, and acetate, common carbon sources in lignocellulose hydrolysate, can boost biomanufacturing economics. However, carbon leaks into biomass biosynthesis pathways instead of the intended target product remain to be optimized. This study aimed to enhance α-carotene production by optimizing glucose, xylose, and acetate utilization in a high-efficiency Corynebacterium glutamicum cell factory. Heterologous xylose pathway expression in C. glutamicum resulted in strain m4, exhibiting a two-fold increase in α-carotene production from xylose compared to glucose. Xylose utilization was found to boost the biosynthesis of pyruvate and acetyl-CoA, essential precursors for carotenoid biosynthesis. Additionally, metabolic engineering including pck, pyc, ppc, and aceE deletion, completely disrupted the metabolic connection between glycolysis and the TCA cycle, further enhancing α-carotene production. This strategic intervention directed glucose and xylose primarily towards target chemical production, while acetate supplied essential metabolites for cell growth recovery. The engineered strain C. glutamicum m8 achieved 30 mg/g α-carotene, 67% higher than strain m4. In fed-batch fermentation, strain m8 produced 1802 mg/L of α-carotene, marking the highest titer reported to date in microbial fermentation. Moreover, it exhibited excellent performance in authentic lignocellulosic hydrolysate, producing 216 mg/L α-carotene, 1.45 times higher than the initial strain (m4). These labor-division strategies significantly contribute to the development of clean processes for producing various valuable chemicals from lignocellulosic resources.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 117-127"},"PeriodicalIF":6.8,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432188","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

Metabolic engineering of Pichia pastoris for overproduction of cis-trans nepetalactol 过量生产顺式-反式新内酯的 Pichia pastoris 代谢工程。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2024-06-17 DOI: 10.1016/j.ymben.2024.06.007

Cuifang Ye , Mengxin Li , Jucan Gao , Yimeng Zuo , Feng Xiao , Xiaojing Jiang , Jintao Cheng , Lei Huang , Zhinan Xu , Jiazhang Lian

{"title":"Metabolic engineering of Pichia pastoris for overproduction of cis-trans nepetalactol","authors":"Cuifang Ye , Mengxin Li , Jucan Gao , Yimeng Zuo , Feng Xiao , Xiaojing Jiang , Jintao Cheng , Lei Huang , Zhinan Xu , Jiazhang Lian","doi":"10.1016/j.ymben.2024.06.007","DOIUrl":"10.1016/j.ymben.2024.06.007","url":null,"abstract":"<div>Monoterpene indole alkaloids (MIAs) are a group of plant-derived natural products with high-value medicinal properties. However, their availability for clinical application is limited due to challenges in plant extraction. Microbial production has emerged as a promising strategy to meet the clinical demands for MIAs. The biosynthetic pathway of cis-trans nepetalactol, which serves as the universal iridoid scaffold for all MIAs, has been successfully identified and reconstituted. However, bottlenecks and challenges remain to construct a high-yielding platform strain for cis-trans nepetalactol production, which is vital for subsequent MIAs biosynthesis. In the present study, we focused on engineering of Pichia pastoris cell factories to enhance the production of geraniol, 8-hydroxygeraniol, and cis-trans nepetalactol. By targeting the biosynthetic pathway from acetyl-CoA to geraniol in both peroxisomes and cytoplasm, we achieved comparable geraniol titers in both compartments. Through protein engineering, we found that either G8H or CPR truncation increased the production of 8-hydroxygeraniol, with a 47.8-fold and 14.0-fold increase in the peroxisomal and cytosolic pathway strain, respectively. Furthermore, through a combination of dynamical control of ERG20, precursor and cofactor supply engineering, diploid engineering, and dual subcellular compartmentalization engineering, we achieved the highest ever reported production of cis-trans nepetalactol, with a titer of 4429.4 mg/L using fed-batch fermentation in a 5-L bioreactor. We anticipate our systematic metabolic engineering strategies to facilitate the development of P. pastoris cell factories for sustainable production of MIAs and other plant natural products.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 83-94"},"PeriodicalIF":6.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141427192","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

Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression 代谢和表达的基因组尺度模型可预测重组蛋白表达的代谢负担。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2024-06-15 DOI: 10.1016/j.ymben.2024.06.005

Omid Oftadeh, Vassily Hatzimanikatis

{"title":"Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression","authors":"Omid Oftadeh, Vassily Hatzimanikatis","doi":"10.1016/j.ymben.2024.06.005","DOIUrl":"10.1016/j.ymben.2024.06.005","url":null,"abstract":"<div>The production of recombinant proteins in a host using synthetic constructs such as plasmids comes at the cost of detrimental effects such as reduced growth, energetic inefficiencies, and other stress responses, collectively known as metabolic burden. Increasing the number of copies of the foreign gene increases the metabolic load but increases the expression of the foreign protein. Thus, there is a trade-off between biomass and product yield in response to changes in heterologous gene copy number. This work proposes a computational method, rETFL (recombinant Expression and Thermodynamic Flux), for analyzing and predicting the responses of recombinant organisms to the introduction of synthetic constructs. rETFL is an extension to the ETFL formulations designed to reconstruct models of metabolism and expression (ME-models). We have illustrated the capabilities of the method in four studies to (i) capture the growth reduction in plasmid-containing E. coli and recombinant protein production; (ii) explore the trade-off between biomass and product yield as plasmid copy number is varied; (iii) predict the emergence of overflow metabolism in recombinant E. coli in agreement with experimental data; and (iv) investigate the individual pathways and enzymes affected by the presence of the plasmid. We anticipate that rETFL will serve as a comprehensive platform for integrating available omics data for recombinant organisms and making context-specific predictions that can help optimize recombinant expression systems for biopharmaceutical production and gene therapy.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 109-116"},"PeriodicalIF":6.8,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141331388","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

Developing a novel heme biosensor to produce high-active hemoproteins in Pichia pastoris through comparative transcriptomics 通过比较转录组学，开发一种新型血红素生物传感器，在 Pichia pastoris 中生产高活性血蛋白。

IF 8.4 1区生物学

Metabolic engineering Pub Date : 2024-06-04 DOI: 10.1016/j.ymben.2024.06.002

Fei Yu , Chenyang Li , Tao Zhang , Jingwen Zhou , Jianghua Li , Jian Chen , Guocheng Du , Xinrui Zhao

{"title":"Developing a novel heme biosensor to produce high-active hemoproteins in Pichia pastoris through comparative transcriptomics","authors":"Fei Yu , Chenyang Li , Tao Zhang , Jingwen Zhou , Jianghua Li , Jian Chen , Guocheng Du , Xinrui Zhao","doi":"10.1016/j.ymben.2024.06.002","DOIUrl":"10.1016/j.ymben.2024.06.002","url":null,"abstract":"<div>The development of a heme-responsive biosensor for dynamic pathway regulation in eukaryotes has never been reported, posing a challenge for achieving the efficient synthesis of multifunctional hemoproteins and maintaining intracellular heme homeostasis. Herein, a biosensor containing a newly identified heme-responsive promoter, CRISPR/dCas9, and a degradation tag N-degron was designed and optimized to fine-tune heme biosynthesis in the efficient heme-supplying Pichia pastoris P1H9 chassis. After identifying literature-reported promoters insensitive to heme, the endogenous heme-responsive promoters were mined by transcriptomics, and an optimal biosensor was screened from different combinations of regulatory elements. The dynamic regulation pattern of the biosensor was validated by the transcriptional fluctuations of the HEM2 gene involved in heme biosynthesis and the subsequent responsive changes in intracellular heme titers. We demonstrate the efficiency of this regulatory system by improving the production of high-active porcine myoglobin and soy hemoglobin, which can be used to develop artificial meat and artificial metalloenzymes. Moreover, these findings can offer valuable strategies for the synthesis of other hemoproteins.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 59-68"},"PeriodicalIF":8.4,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262288","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

Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida 利用假单胞菌生产抗衰老防晒化合物的系统工程。

IF 8.4 1区生物学

Metabolic engineering Pub Date : 2024-06-03 DOI: 10.1016/j.ymben.2024.06.001

Ian S. Yunus , Graham A. Hudson , Yan Chen , Jennifer W. Gin , Joonhoon Kim , Edward E.K. Baidoo , Christopher J. Petzold , Paul D. Adams , Blake A. Simmons , Aindrila Mukhopadhyay , Jay D. Keasling , Taek Soon Lee

{"title":"Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida","authors":"Ian S. Yunus , Graham A. Hudson , Yan Chen , Jennifer W. Gin , Joonhoon Kim , Edward E.K. Baidoo , Christopher J. Petzold , Paul D. Adams , Blake A. Simmons , Aindrila Mukhopadhyay , Jay D. Keasling , Taek Soon Lee","doi":"10.1016/j.ymben.2024.06.001","DOIUrl":"10.1016/j.ymben.2024.06.001","url":null,"abstract":"<div>Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO2 has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an efficient microbial platform for production of shinorine, a UV light absorbing compound with anti-aging properties. First, we methodically selected an appropriate host for shinorine production by analyzing central carbon flux distribution data from prior studies alongside predictions from genome-scale metabolic models (GEMs). We enhanced shinorine productivity through CRISPRi-mediated downregulation and utilized shotgun proteomics to pinpoint potential competing pathways. Simultaneously, we improved the shinorine biosynthetic pathway by refining its design, optimizing promoter usage, and altering the strength of ribosome binding sites. Finally, we conducted amino acid feeding experiments under various conditions to identify the key limiting factors in shinorine production. The study combines meta-analysis of 13C-metabolic flux analysis, GEMs, synthetic biology, CRISPRi-mediated gene downregulation, and omics analysis to improve shinorine production, demonstrating the potential of Pseudomonas putida KT2440 as platform for shinorine production.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 69-82"},"PeriodicalIF":8.4,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1096717624000740/pdfft?md5=44465b68d63fbfbca8dde006226cbcc1&pid=1-s2.0-S1096717624000740-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262290","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}

引用次数: 0

Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering 通过知识丰富的转录组学解密营养压力反应，促进微生物工程。

IF 8.4 1区生物学

Metabolic engineering Pub Date : 2024-05-31 DOI: 10.1016/j.ymben.2024.05.007

Jongoh Shin , Daniel C. Zielinski , Bernhard O. Palsson

{"title":"Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering","authors":"Jongoh Shin , Daniel C. Zielinski , Bernhard O. Palsson","doi":"10.1016/j.ymben.2024.05.007","DOIUrl":"10.1016/j.ymben.2024.05.007","url":null,"abstract":"<div>Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research and biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress responses of Vibrio natriegens to supplied nutrients, aiming to enhance microbial engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across a comprehensive transcriptomics dataset containing a broad array of nutrient conditions. Our approach led to the i) identification of novel transporter systems for diverse substrates, ii) a detailed understanding of how trace elements affect metabolism and growth, and iii) extensive characterization of nutrient-induced stress responses, including osmotic stress, low glycolytic flux, proteostasis, and altered protein expression. By clarifying the relationship between the acetate-associated regulon and glycolytic flux status of various nutrients, we have showcased its vital role in directing optimal carbon source selection. Our findings offer deep insights into the transcriptional landscape of bacterial nutrition and underscore its significance in tailoring strain engineering strategies, thereby facilitating the development of more efficient and robust microbial systems for biotechnological applications.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 34-47"},"PeriodicalIF":8.4,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1096717624000739/pdfft?md5=a9bd2ce014a1acf27200571667e42fcc&pid=1-s2.0-S1096717624000739-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141200284","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}

引用次数: 0

De novo biosynthesis of 3-hydroxy-3-methylbutyrate as anti-catabolic supplement by metabolically engineered Escherichia coli 3-羟基-3-甲基丁酸作为抗分解代谢补充剂的新生物合成。

IF 8.4 1区生物学

Metabolic engineering Pub Date : 2024-05-28 DOI: 10.1016/j.ymben.2024.05.006

Sally J. Huang , Martin J. Lai , Arvin Y. Chen , Ethan I. Lan

{"title":"De novo biosynthesis of 3-hydroxy-3-methylbutyrate as anti-catabolic supplement by metabolically engineered Escherichia coli","authors":"Sally J. Huang , Martin J. Lai , Arvin Y. Chen , Ethan I. Lan","doi":"10.1016/j.ymben.2024.05.006","DOIUrl":"10.1016/j.ymben.2024.05.006","url":null,"abstract":"<div>3-Hydroxy-3-methylbutyrate (HMB) is a five-carbon branch-chain hydroxy acid currently used as a dietary supplement to treat sarcopenia and exercise training. However, its current production relies on conventional chemical processes which require toxic substances and are generally non-sustainable. While bio-based syntheses of HMB have been developed, they are dependent on biotransformation of its direct precursors which are generally costly. Therefore, in this work, we developed a synthetic de novo HMB biosynthetic pathway that enables HMB production from renewable resources. This novel HMB biosynthesis employs heterologous enzymes from mevalonate pathway and myxobacterial iso-fatty acid pathway for converting acetyl-CoA to HMB-CoA. Subsequently, HMB-CoA is hydrolyzed by a thioesterase to yield HMB. Upon expression of this pathway, our initial Escherichia coli strain produced 660 mg/L of HMB from glucose in 48 hours. Through optimization of coenzyme A removal from HMB-CoA and genetic operon structure, our final strain achieved HMB production titer of 17.7 g/L in glucose minimal media using a bench-top bioreactor. This engineered strain was further demonstrated to produce HMB from other renewable carbon sources such as xylose, glycerol, and acetate. The results from this work provided a flexible and environmentally benign method for producing HMB.</div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"84 ","pages":"Pages 48-58"},"PeriodicalIF":8.4,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175543","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