Metabolic Engineering Communications最新文献_第2页

Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440 利用转基因恶臭假单胞菌KT2440合成有价吡嗪衍生物的微生物合成途径

IF 3.7

Metabolic Engineering Communications Pub Date : 2025-06-01 Epub Date: 2025-03-30 DOI: 10.1016/j.mec.2025.e00258

Vytautas Petkevičius, Justė Juknevičiūtė, Domas Mašonis, Rolandas Meškys

{"title":"Synthetic pathways for microbial biosynthesis of valuable pyrazine derivatives using genetically modified Pseudomonas putida KT2440","authors":"Vytautas Petkevičius, Justė Juknevičiūtė, Domas Mašonis, Rolandas Meškys","doi":"10.1016/j.mec.2025.e00258","DOIUrl":"10.1016/j.mec.2025.e00258","url":null,"abstract":"<div><div>Using engineered microbes for synthesizing high-valued chemicals from renewable sources is a foundation in synthetic biology, however, it is still in its early stages. Here, we present peculiarities and troubleshooting of the construction of novel synthetic metabolic pathways in genetically modified work-horse Pseudomonas putida KT2440. The combination of this microbial host and heterologous expressed non-heme diiron monooxygenases enabled de novo biosynthesis of 2,5-dimethylpyrazine (2,5-DMP) carboxylic acid and N-oxides as target products. A key intermediate, 2,5-DMP, was obtained by using Pseudomonas putida KT2440Δ6 strain containing six gene deletions in the L-threonine pathway, along with the overexpression of thrAS345F and tdh from E. coli. Thus, the carbon surplus was redirected from glucose through L-threonine metabolism toward the formation of 2,5-DMP, resulting in a product titre of 106 ± 30 mg L−1. By introducing two native genes (thrB and thrC from P. putida KT2440) from the L-threonine biosynthesis pathway, the production of 2,5-DMP was increased to 168 ± 20 mg L−1. The resulting 2,5-DMP was further derivatized through two separate pathways. Recombinant P. putida KT2440 strain harboring xylene monooxygenase (XMO) produced 5-methyl-2-pyrazinecarboxylic acid from glucose as a targeted compound in a product titre of 204 ± 24 mg L−1. The microbial host containing genes of PmlABCDEF monooxygenase (Pml) biosynthesized N-oxides – 2,5-dimethylpyrazine 1-oxide as a main product, and 2,5-dimethylpyrazine 1,4-dioxide as a minor product, reaching product titres of 82 ± 8 mg L−1 and 11 ± 2 mg L−1 respectively.</div></div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"20 ","pages":"Article e00258"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143748119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Production of borneol, camphor, and bornyl acetate using engineered Saccharomyces cerevisiae 利用工程酿酒酵母生产冰片、樟脑和冰片醋酸酯

IF 3.7

Metabolic Engineering Communications Pub Date : 2025-06-01 Epub Date: 2025-03-31 DOI: 10.1016/j.mec.2025.e00259

Masahiro Tominaga , Kazuma Kawakami , Hiro Ogawa , Tomomi Nakamura , Akihiko Kondo , Jun Ishii

{"title":"Production of borneol, camphor, and bornyl acetate using engineered Saccharomyces cerevisiae","authors":"Masahiro Tominaga , Kazuma Kawakami , Hiro Ogawa , Tomomi Nakamura , Akihiko Kondo , Jun Ishii","doi":"10.1016/j.mec.2025.e00259","DOIUrl":"10.1016/j.mec.2025.e00259","url":null,"abstract":"<div><div>Microbial production of bicyclic monoterpenes is of great interest because their production primarily utilizes non-sustainable resources. Here, we report an engineered Saccharomyces cerevisiae yeast that produces bicyclic monoterpenes, including borneol, camphor, and bornyl acetate. The engineered yeast expresses a bornyl pyrophosphatase synthase from Salvia officinalis fused with mutated farnesyl pyrophosphate synthase from S. cerevisiae and two mevalonate pathway enzymes (an acetoacetyl-CoA thiolase/hydroxymethylglutaryl-CoA [HMG-CoA] reductase and an HMG-CoA synthase) from Enterococcus faecalis. The yeast produced up to 23.0 mg/L of borneol in shake-flask fermentation. By additionally expressing borneol dehydrogenase from Pseudomonas sp. TCU-HL1 or bornyl acetyltransferase from Wurfbainia villosa, the engineered yeast produced 23.5 mg/L of camphor and 21.1 mg/L of bornyl acetate, respectively. This is the first report of heterologous production of camphor and bornyl acetate.</div></div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"20 ","pages":"Article e00259"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143767910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering Pseudomonas putida for production of 3-hydroxyacids using hybrid type I polyketide synthases 利用杂交I型聚酮合成酶生产3-羟基酸的工程恶臭假单胞菌

IF 3.7

Metabolic Engineering Communications Pub Date : 2025-06-01 Epub Date: 2025-04-02 DOI: 10.1016/j.mec.2025.e00261

Matthias Schmidt , Aaron A. Vilchez , Namil Lee , Leah S. Keiser , Allison N. Pearson , Mitchell G. Thompson , Yolanda Zhu , Robert W. Haushalter , Adam M. Deutschbauer , Satoshi Yuzawa , Lars M. Blank , Jay D. Keasling

{"title":"Engineering Pseudomonas putida for production of 3-hydroxyacids using hybrid type I polyketide synthases","authors":"Matthias Schmidt , Aaron A. Vilchez , Namil Lee , Leah S. Keiser , Allison N. Pearson , Mitchell G. Thompson , Yolanda Zhu , Robert W. Haushalter , Adam M. Deutschbauer , Satoshi Yuzawa , Lars M. Blank , Jay D. Keasling","doi":"10.1016/j.mec.2025.e00261","DOIUrl":"10.1016/j.mec.2025.e00261","url":null,"abstract":"<div><div>Engineered type I polyketide synthases (T1PKSs) are a potentially transformative platform for the biosynthesis of small molecules. Due to their modular nature, T1PKSs can be rationally designed to produce a wide range of bulk or specialty chemicals. While heterologous PKS expression is best studied in microbes of the genus Streptomyces, recent studies have focused on the exploration of non-native PKS hosts. The biotechnological production of chemicals in fast growing and industrial relevant hosts has numerous economic and logistic advantages. With its native ability to utilize alternative feedstocks, Pseudomonas putida has emerged as a promising workhorse for the sustainable production of small molecules. Here, we outline the assessment of P. putida as a host for the expression of engineered T1PKSs and production of 3-hydroxyacids. After establishing the functional expression of an engineered T1PKS, we successfully expanded and increased the pool of available acyl-CoAs needed for the synthesis of polyketides using transposon sequencing and protein degradation tagging. This work demonstrates the potential of T1PKSs in P. putida as a production platform for the sustainable biosynthesis of unnatural polyketides.</div></div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"20 ","pages":"Article e00261"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-step pathway engineering in probiotic Saccharomyces boulardii for abscisic acid production in the gut 益生菌博氏酵母菌肠道脱落酸生产的多步骤途径工程

IF 3.7

Metabolic Engineering Communications Pub Date : 2025-06-01 Epub Date: 2025-05-30 DOI: 10.1016/j.mec.2025.e00263

Femke Van Gaever , Paul Vandecruys , Yasmine Driege , Seo Woo Kim , Johan M. Thevelein , Rudi Beyaert , Jens Staal

{"title":"Multi-step pathway engineering in probiotic Saccharomyces boulardii for abscisic acid production in the gut","authors":"Femke Van Gaever , Paul Vandecruys , Yasmine Driege , Seo Woo Kim , Johan M. Thevelein , Rudi Beyaert , Jens Staal","doi":"10.1016/j.mec.2025.e00263","DOIUrl":"10.1016/j.mec.2025.e00263","url":null,"abstract":"<div><div>The plant hormone abscisic acid (ABA) has gained attention for its role in animals and humans, particularly due to its protective effects in various immune and inflammatory disorders. Given its high concentrations in fruits like figs, bilberries and apricots, ABA shows promise as a nutraceutical. However scalability, short half-life and cost limit the use of ABA-enriched fruit extracts and synthetic supplements. In this study, we propose an alternative ABA administration method to overcome these challenges. We genetically engineered a strain of the probiotic Saccharomyces boulardii to produce and deliver ABA directly to the gut of mice. Using the biosynthesis pathway from Botrytis cinerea, four genes (bcaba1-4) were integrated into S. boulardii, enabling ABA production at 30 °C, as previously described in Saccharomyces cerevisiae. Introducing an additional cytochrome P450 reductase gene resulted in a 7-fold increase in ABA titers, surpassing previous ABA-producing S. cerevisiae strains. Supplementation of the ABA-producing S. boulardii in the diet of mice (at a concentration of 5 × 108 CFU/g) led to effective gut colonization but resulted in low serum ABA levels (approximately 1.8 ng/mL). The absence of detectable serum ABA after administration of the ABA-producing probiotic through oral gavage, prompted further investigation to determine the underlying cause. The physiological body temperature (37 °C) was identified as a major bottleneck for ABA production. Modifications to enhance the mevalonate pathway flux improved ABA levels at 37 °C. However, additional modifications are needed to optimize ABA production before testing this probiotic in disease contexts in mice.</div></div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"20 ","pages":"Article e00263"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144231628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

13C-metabolic flux analysis of Saccharomyces cerevisiae in complex media 酵母在复杂培养基中的13c代谢通量分析

IF 3.7

Metabolic Engineering Communications Pub Date : 2025-06-01 Epub Date: 2025-04-01 DOI: 10.1016/j.mec.2025.e00260

Hayato Fujiwara , Nobuyuki Okahashi , Taisuke Seike , Fumio Matsuda

{"title":"13C-metabolic flux analysis of Saccharomyces cerevisiae in complex media","authors":"Hayato Fujiwara , Nobuyuki Okahashi , Taisuke Seike , Fumio Matsuda","doi":"10.1016/j.mec.2025.e00260","DOIUrl":"10.1016/j.mec.2025.e00260","url":null,"abstract":"<div><div>Saccharomyces cerevisiae is often cultivated in complex media for applications in food and other biochemical production. However, 13C-metabolic flux analysis (13C-MFA) has been conducted for S. cerevisiae cultivated in synthetic media, resulting in a limited understanding of the metabolic flux distributions under the complex media. In this study, 13C-MFA was applied to S. cerevisiae cultivated in complex media to quantify the metabolic fluxes in the central metabolic network. S. cerevisiae was cultivated in a synthetic dextrose (SD) medium supplemented with 20 amino acids (SD + AA) and yeast extract peptone dextrose (YPD) medium. The results revealed that glutamic acid, glutamine, aspartic acid, and asparagine are incorporated into the TCA cycle as carbon sources in parallel with glucose consumption. Based on these findings, we successfully conducted 13C-MFA of S. cerevisiae cultivated in SD + AA and YPD media using parallel labeling and measured amino acid uptake rates. Furthermore, we applied the developed approach to 13C-MFA of yeast cultivated in malt extract medium. The analysis revealed that the metabolic flux through the anaplerotic and oxidative pentose phosphate pathways was lower in complex media than in synthetic media. Owing to the reduced carbon loss by the branching pathways, carbon flow toward ethanol production via glycolysis could be elevated. 13C-MFA of S. cerevisiae cultured in complex media provides valuable insights for metabolic engineering and process optimization in industrial yeast fermentation.</div></div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"20 ","pages":"Article e00260"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143791672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Production of (R)-citramalate by engineered Saccharomyces cerevisiae 利用工程酿酒酵母生产(R)-柠檬酸盐

IF 3.7

Metabolic Engineering Communications Pub Date : 2024-12-01 Epub Date: 2024-08-10 DOI: 10.1016/j.mec.2024.e00247

Ryosuke Mitsui , Akihiko Kondo , Tomokazu Shirai

{"title":"Production of (R)-citramalate by engineered Saccharomyces cerevisiae","authors":"Ryosuke Mitsui , Akihiko Kondo , Tomokazu Shirai","doi":"10.1016/j.mec.2024.e00247","DOIUrl":"10.1016/j.mec.2024.e00247","url":null,"abstract":"<div>The budding yeast, Saccharomyces cerevisiae, has a high tolerance to organic acids and alcohols, and thus grows well under toxic concentrations of various compounds in the culture medium, potentially allowing for highly efficient compound production. (R)-citramalate is a raw material for methyl methacrylate and can be used as a metabolic intermediate in the biosynthesis of higher alcohols. (R)-citramalate is synthesized from pyruvate and acetyl-CoA. Unlike Escherichia coli, S. cerevisiae has organelles, and its intracellular metabolites are compartmentalized, preventing full use of intracellular acetyl-CoA. Therefore, in this study, to increase the amount of cytosolic acetyl-CoA for highly efficient production of (R)-citramalate, we inhibited the transport of cytosolic acetyl-CoA and pyruvate to the mitochondria. We also constructed a heterologous pathway to supply cytosolic acetyl-CoA. Additionally, we attempted to export (R)-citramalate from cells by expressing a heterologous dicarboxylate transporter gene. We evaluated the effects of these approaches on (R)-citramalate production and constructed a final strain by combining these positive approaches. The resulting strain produced 16.5 mM (R)-citramalate in batch culture flasks. This is the first report of (R)-citramalate production by recombinant S. cerevisiae, and the (R)-citramalate production by recombinant yeast achieved in this study was the highest reported to date.</div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"19 ","pages":"Article e00247"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214030124000166/pdfft?md5=8e77960467f6df90982ae565f50fc7ce&pid=1-s2.0-S2214030124000166-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141985411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum 热梭菌中单功能醇脱氢酶的表达和特性分析

IF 3.7

Metabolic Engineering Communications Pub Date : 2024-12-01 Epub Date: 2024-06-20 DOI: 10.1016/j.mec.2024.e00243

Daniela Prates Chiarelli , Bishal Dev Sharma , Shuen Hon , Luana Walravens Bergamo , Lee R. Lynd , Daniel G. Olson

{"title":"Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum","authors":"Daniela Prates Chiarelli , Bishal Dev Sharma , Shuen Hon , Luana Walravens Bergamo , Lee R. Lynd , Daniel G. Olson","doi":"10.1016/j.mec.2024.e00243","DOIUrl":"https://doi.org/10.1016/j.mec.2024.e00243","url":null,"abstract":"<div>Clostridium thermocellum is a thermophilic anaerobic bacterium that could be used for cellulosic biofuel production due to its strong native ability to consume cellulose, however its ethanol production ability needs to be improved to enable commercial application. In our previous strain engineering work, we observed a spontaneous mutation in the native adhE gene that reduced ethanol production. Here we attempted to complement this mutation by heterologous expression of 18 different alcohol dehydrogenase (adh) genes. We were able to express all of them successfully in C. thermocellum. Surprisingly, however, none of them increased ethanol production, and several actually decreased it. Our findings contribute to understanding the correlation between C. thermocellum ethanol production and Adh enzyme cofactor preferences. The identification of a set of adh genes that can be successfully expressed in this organism provides a foundation for future investigations into how the properties of Adh enzymes affect ethanol production.</div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"19 ","pages":"Article e00243"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214030124000129/pdfft?md5=5d222b62409146f886808888e57c6440&pid=1-s2.0-S2214030124000129-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141480759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering thioesterase as a driving force for novel itaconate production via its degradation scheme 工程硫酯酶是通过其降解方案生产新型伊塔康酸的驱动力

IF 3.7

Metabolic Engineering Communications Pub Date : 2024-12-01 Epub Date: 2024-08-05 DOI: 10.1016/j.mec.2024.e00246

Ryan S. Wang, Siang-Wun Siao, Jessica C. Wang, Patrick Y. Lin, Claire R. Shen

{"title":"Engineering thioesterase as a driving force for novel itaconate production via its degradation scheme","authors":"Ryan S. Wang, Siang-Wun Siao, Jessica C. Wang, Patrick Y. Lin, Claire R. Shen","doi":"10.1016/j.mec.2024.e00246","DOIUrl":"10.1016/j.mec.2024.e00246","url":null,"abstract":"<div>Incorporation of irreversible steps in pathway design enhances the overall thermodynamic favorability and often leads to better bioconversion yield given functional enzymes. Using this concept, here we constructed the first non-natural itaconate biosynthesis pathway driven by thioester hydrolysis. Itaconate is a commercially valuable platform chemical with wide applications in the synthetic polymer industry. Production of itaconate has long relied on the decarboxylation of TCA cycle intermediate cis-aconitate as the only biosynthetic route. Inspired by nature's design of itaconate detoxification, here we engineered a novel itaconate producing pathway orthogonal to native metabolism with no requirement of auxotrophic knock-out. The reversed degradation pathway initiates with pyruvate and acetyl-CoA condensation forming (S)-citramalyl-CoA, followed by its dehydration and isomerization into itaconyl-CoA then hydrolysis into itaconate. Phenylacetyl-CoA thioesterase (PaaI) from Escherichia coli was identified via screening to deliver the highest itaconate formation efficiency when coupled to the reversible activity of citramalate lyase and itaconyl-CoA hydratase. The preference of PaaI towards itaconyl-CoA hydrolysis over acetyl-CoA and (S)-citramalyl-CoA also minimized the inevitable precursor loss due to enzyme promiscuity. With acetate recycling, acetyl-CoA conservation, and condition optimization, we achieved a final itaconate titer of 1 g/L using the thioesterase driven pathway, which is a significant improvement compared to the original degradation pathway based on CoA transferase. This study illustrates the significance of thermodynamic favorability as a design principle in pathway engineering.</div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"19 ","pages":"Article e00246"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214030124000154/pdfft?md5=8638d3ac45e484bb976c59dea9cff40b&pid=1-s2.0-S2214030124000154-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141963669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CFSA: Comparative flux sampling analysis as a guide for strain design CFSA：作为应变设计指南的通量取样比较分析

IF 3.7

Metabolic Engineering Communications Pub Date : 2024-12-01 Epub Date: 2024-06-24 DOI: 10.1016/j.mec.2024.e00244

R.P. van Rosmalen , S. Moreno-Paz , Z.E. Duman-Özdamar, M. Suarez-Diez

{"title":"CFSA: Comparative flux sampling analysis as a guide for strain design","authors":"R.P. van Rosmalen , S. Moreno-Paz , Z.E. Duman-Özdamar, M. Suarez-Diez","doi":"10.1016/j.mec.2024.e00244","DOIUrl":"https://doi.org/10.1016/j.mec.2024.e00244","url":null,"abstract":"<div>Genome-scale metabolic models of microbial metabolism have extensively been used to guide the design of microbial cell factories, still, many of the available strain design algorithms often fail to produce a reduced list of targets for improved performance that can be implemented and validated in a step-wise manner. We present Comparative Flux Sampling Analysis (CFSA), a strain design method based on the extensive comparison of complete metabolic spaces corresponding to maximal or near-maximal growth and production phenotypes. The comparison is complemented by statistical analysis to identify reactions with altered flux that are suggested as targets for genetic interventions including up-regulations, down-regulations and gene deletions. We applied CFSA to the production of lipids by Cutaneotrichosporon oleaginosus and naringenin by Saccharomyces cerevisiae identifying engineering targets in agreement with previous studies as well as new interventions. CFSA is an easy-to-use, robust method that suggests potential metabolic engineering targets for growth-uncoupled production that can be applied to the design of microbial cell factories.</div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"19 ","pages":"Article e00244"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2214030124000130/pdfft?md5=69d0fb5da6998ef5e347063552f98736&pid=1-s2.0-S2214030124000130-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141542319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reconstruction and analyses of genome-scale halomonas metabolic network yield a highly efficient PHA production 基因组尺度卤单胞菌代谢网络的重建和分析产生了高效的 PHA 生产

IF 3.7

Metabolic Engineering Communications Pub Date : 2024-12-01 Epub Date: 2024-11-19 DOI: 10.1016/j.mec.2024.e00251

Luhui Zhang , Xinpei Sun , Jianwen Ye , QianQian Yuan , Xin Zhang , Fei Sun , Yongpan An , Yutong Chen , Yuehui Qian , Daqian Yang , Qian Wang , Miaomiao Gao , Tao Chen , Hongwu Ma , Guoqiang Chen , Zhengwei Xie

{"title":"Reconstruction and analyses of genome-scale halomonas metabolic network yield a highly efficient PHA production","authors":"Luhui Zhang , Xinpei Sun , Jianwen Ye , QianQian Yuan , Xin Zhang , Fei Sun , Yongpan An , Yutong Chen , Yuehui Qian , Daqian Yang , Qian Wang , Miaomiao Gao , Tao Chen , Hongwu Ma , Guoqiang Chen , Zhengwei Xie","doi":"10.1016/j.mec.2024.e00251","DOIUrl":"10.1016/j.mec.2024.e00251","url":null,"abstract":"<div><div>In pursuit of reliable and efficient industrial microbes, this study integrates cutting-edge systems biology tools with Halomonas bluephagenesis TD01, a robust halophilic bacterium. We generated the complete and annotated circular genome sequence for this model organism, constructed and meticulously curated a genome-scale metabolic network, achieving striking 86.32% agreement with Biolog Phenotype Microarray data and visualize the network via an interactive Electron/Thrift server architecture. We then analyzed the genome-scale network using vertex sampling analysis (VSA) and found that productions of biomass, polyhydroxyalkanoates (PHA), citrate, acetate, and pyruvate are mutually competing. Recognizing the dynamic nature of H. bluephagenesis TD01, we further developed and implemented the hyper-cube-shrink-analysis (HCSA) framework to predict effects of nutrient availabilities and metabolic reactions in the model on biomass and PHA accumulation. We then, based on the analysis results, proposed and validate multi-step feeding strategies tailored to different fermentation stages. This integrated approach yielded remarkable results, with fermentation culminating in a cell dry weight of 100.4 g/L and 70% PHA content, surpassing previous benchmarks. Our findings exemplify the powerful potential of system-level tools in the design and optimization of industrial microorganisms, paving the way for more efficient and sustainable bio-based processes.</div></div>","PeriodicalId":18695,"journal":{"name":"Metabolic Engineering Communications","volume":"19 ","pages":"Article e00251"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142707018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0