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Corrigendum to “Cyclo-diphenylalanine Production in Aspergillus nidulans through Stepwise Metabolic Engineering” [Metab. Eng. 82 (2024) 147–156] Metab. Eng. (IF 8.4) Pub Date : 2024-03-11 Xiaolin Liu, Kang Li, Jing Yu, Chuanteng Ma, Qian Che, Tianjiao Zhu, Dehai Li, Blaine A. Pfeifer, Guojian Zhang
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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Metab. Eng. (IF 8.4) Pub Date : 2024-03-08 Maxime Lecomte, Wenfan Cao, Julie Aubert, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe
Cheese taste and flavour properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting of , and during a seven-week cheese
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Elucidating uptake and metabolic fate of dipeptides in CHO cell cultures using 13C labeling experiments and kinetic modeling Metab. Eng. (IF 8.4) Pub Date : 2024-03-07 Harnish Mukesh Naik, Xiangchen Cai, Pranay Ladiwala, Jayanth Venkatarama Reddy, Michael J. Betenbaugh, Maciek R. Antoniewicz
The rapidly growing market of biologics including monoclonal antibodies has stimulated the need to improve biomanufacturing processes including mammalian host systems such as Chinese Hamster Ovary (CHO) cells. Cell culture media formulations continue to be enhanced to enable intensified cell culture processes and optimize cell culture performance. Amino acids, major components of cell culture media
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Leveraging a Y. lipolytica naringenin chassis for biosynthesis of apigenin and associated glucoside Metab. Eng. (IF 8.4) Pub Date : 2024-03-04 Celeste B. Marsan, Sung Gyung Lee, Ankim Nguyen, Angela R. Gordillo Sierra, Sarah M. Coleman, Sierra M. Brooks, Hal S. Alper
Flavonoids are a diverse set of natural products with promising bioactivities including anti-inflammatory, anti-cancer, and neuroprotective properties. Previously, the oleaginous host has been engineered to produce high titers of the base flavonoid naringenin. Here, we leverage this host along with a set of bioconversion strains to produce the flavone apigenin and its glycosylated derivative isovitexin
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High titer production of gastrodin enabled by systematic refactoring of yeast genome and an antisense-transcriptional regulation toolkit Metab. Eng. (IF 8.4) Pub Date : 2024-02-28 Yang Gu, Yaru Jiang, Changfan Li, Jiang Zhu, Xueyao Lu, Jianyue Ge, Mengchen Hu, Jieying Deng, Jingbo Ma, Zhiliang Yang, Xiaoman Sun, Feng Xue, Guocheng Du, Peng Xu, He Huang
Gastrodin, a phenolic glycoside, is a prominent component of , which is renowned for its sedative, hypnotic, anticonvulsant, and neuroprotective activities. Engineering heterologous production of plant natural products in microbial host represents a safe, cost-effective, and scalable alternative to plant extraction. Here, we present the construction of an engineered yeast that achieves a high-titer
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High-level production of Rhodiola rosea characteristic component rosavin from D-glucose and L-arabinose in engineered Escherichia coli Metab. Eng. (IF 8.4) Pub Date : 2024-02-28 Lijun Li, Moshi Liu, Huiping Bi, Tao Liu
Rosavin is the characteristic component of L., an important medicinal plant used widely in the world that has been reported to possess multiple biological activities. However, the endangered status of wild Rhodiola has limited the supply of rosavin. In this work, we successfully engineered an strain to efficiently produce rosavin as an alternative production method. Firstly, cinnamate: CoA ligase from
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Genome-wide host-pathway interactions affecting cis-cis-muconic acid production in yeast Metab. Eng. (IF 8.4) Pub Date : 2024-02-28 Paul Cachera, Nikolaj Can Kurt, Andreas Røpke, Tomas Strucko, Uffe H. Mortensen, Michael K. Jensen
The success of forward metabolic engineering depends on a thorough understanding of the behaviour of a heterologous metabolic pathway within its host. We have recently described CRI-SPA, a high-throughput gene editing method enabling the delivery of a metabolic pathway to all strains of the knock-out library. CRI-SPA systematically quantifies the effect of each modified gene present in the library
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Ectoine hyperproduction by engineered Halomonas bluephagenesis Metab. Eng. (IF 8.4) Pub Date : 2024-02-23 Qitiao Hu, Simian Sun, Zhongnan Zhang, Wei Liu, Xueqing Yi, Hongtao He, Nigel S. Scrutton, Guo-Qiang Chen
Ectoine, a crucial osmoprotectant for salt adaptation in halophiles, has gained growing interest in cosmetics and medical industries. However, its production remains challenged by stringent fermentation process in model microorganisms and low production level in its native producers. Here, we systematically engineered the native ectoine producer for ectoine production by overexpressing operon, increasing
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Machine learning predicts system-wide metabolic flux control in cyanobacteria Metab. Eng. (IF 8.4) Pub Date : 2024-02-21 Amit Kugler, Karin Stensjö
Metabolic fluxes and their control mechanisms are fundamental in cellular metabolism, offering insights for the study of biological systems and biotechnological applications. However, quantitative and predictive understanding of controlling biochemical reactions in microbial cell factories, especially at the system level, is limited. In this work, we present ARCTICA, a computational framework that
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Cyclo-diphenylalanine production in Aspergillus nidulans through stepwise metabolic engineering Metab. Eng. (IF 8.4) Pub Date : 2024-02-20 Xiaolin Liu, Kang Li, Jing Yu, Chuanteng Ma, Qian Che, Tianjiao Zhu, Dehai Li, Blaine A. Pfeifer, Guojian Zhang
Cyclo-diphenylalanine (cFF) is a symmetrical aromatic diketopiperazine (DKP) found wide-spread in microbes, plants, and resulting food products. As different bioactivities continue being discovered and relevant food and pharmaceutical applications gradually emerge for cFF, there is a growing need for establishing convenient and efficient methods to access this type of compound. Here, we present a robust
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Combinatorial biosynthesis in yeast leads to over 200 diterpenoids Metab. Eng. (IF 8.4) Pub Date : 2024-02-20 Maximilian Frey, Ulschan Bathe, Luca Meink, Gerd U. Balcke, Jürgen Schmidt, Andrej Frolov, Alena Soboleva, Ahmed Hassanin, Mehdi D. Davari, Oliver Frank, Verena Schlagbauer, Corinna Dawid, Alain Tissier
Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. The modular character of diterpene biosynthesis and the promiscuity of the enzymes involved make combinatorial biosynthesis a promising approach to generate libraries of diverse diterpenoids. Here, we report on the combinatorial assembly in yeast of ten diterpene synthases
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COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling Metab. Eng. (IF 8.4) Pub Date : 2024-02-20 Saratram Gopalakrishnan, William Johnson, Miguel A. Valderrama-Gomez, Elcin Icten, Jasmine Tat, Michael Ingram, Coral Fung Shek, Pik K. Chan, Fabrice Schlegel, Pablo Rolandi, Cleo Kontoravdi, Nathan E. Lewis
Metabolism governs cell performance in biomanufacturing, as it fuels growth and productivity. However, even in well-controlled culture systems, metabolism is dynamic, with shifting objectives and resources, thus limiting the predictive capability of mechanistic models for process design and optimization. Here, we present Cellular Objectives and State Modulation In bioreaCtors (COSMIC)-dFBA, a hybrid
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Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux Metab. Eng. (IF 8.4) Pub Date : 2024-02-20 Joseph Christian Utomo, Hailey Brynn Barrell, Rahul Kumar, Jessica Smith, Maximilian Simon Brant, Hector De la Hoz Siegler, Dae-Kyun Ro
Curcumin is a polyphenolic natural product from the roots of turmeric (). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via -coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis
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Metabolic flux optimization of iterative pathways through orthogonal gene expression control: Application to the β-oxidation reversal Metab. Eng. (IF 8.4) Pub Date : 2024-02-20 Seung Hwan Lee, Yang Hu, Alexander Chou, Jing Chen, Ramon Gonzalez
Balancing relative expression of pathway genes to minimize flux bottlenecks and metabolic burden is one of the key challenges in metabolic engineering. This is especially relevant for iterative pathways, such as reverse β-oxidation (rBOX) pathway, which require control of flux partition at multiple nodes to achieve efficient synthesis of target products. Here, we develop a plasmid-based inducible system
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Corynebacterium glutamicum cell factory design for the efficient production of cis, cis-muconic acid Metab. Eng. (IF 8.4) Pub Date : 2024-02-17 Menglei Li, Jiayao Chen, Keqin He, Changsheng Su, Yilu Wu, Tianwei Tan
Cis, -muconic acid (MA) is widely used as a key starting material in the synthesis of diverse polymers. The growing demand in these industries has led to an increased need for MA. Here, we constructed recombinant by systems metabolic engineering, which exhibit high efficiency in the production of MA. Firstly, the three major degradation pathways were disrupted in the MA production process. Subsequently
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Efficient production of protocatechuic acid using systems engineering of Escherichia coli Metab. Eng. (IF 8.4) Pub Date : 2024-02-16 Ming Wang, Haomiao Wang, Cong Gao, Wanqing Wei, Jia Liu, Xiulai Chen, Guipeng Hu, Wei Song, Jing Wu, Fan Zhang, Liming Liu
Protocatechuic acid (3, 4-dihydroxybenzoic acid, PCA) is widely used in the pharmaceuticals, health food, and cosmetics industries owing to its diverse biological activities. However, the inhibition of 3-dehydroshikimate dehydratase (AroZ) by PCA and its toxicity to cells limit the efficient production of PCA in . In this study, a high-level strain of 3-dehydroshikimate, DHS01, was developed by blocking
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Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida Metab. Eng. (IF 8.4) Pub Date : 2024-02-16 Deepanwita Banerjee, Ian S. Yunus, Xi Wang, Jinho Kim, Aparajitha Srinivasan, Russel Menchavez, Yan Chen, Jennifer W. Gin, Christopher J. Petzold, Hector Garcia Martin, Jon K. Magnuson, Paul D. Adams, Blake A. Simmons, Aindrila Mukhopadhyay, Joonhoon Kim, Taek Soon Lee
Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane) and has been produced in several engineered microorganisms. Recently, has gained interest as a future host for isoprenol bioproduction as it can utilize carbon sources from inexpensive
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Prediction and integration of metabolite-protein interactions with genome-scale metabolic models Metab. Eng. (IF 8.4) Pub Date : 2024-02-15 Mahdis Habibpour, Zahra Razaghi-Moghadam, Zoran Nikoloski
Metabolites, as small molecules, can act not only as substrates to enzymes, but also as effectors of activity of proteins with different functions, thereby affecting various cellular processes. While several experimental techniques have started to catalogue the metabolite-protein interactions (MPIs) present in different cellular contexts, characterizing the functional relevance of MPIs remains a challenging
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Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth Metab. Eng. (IF 8.4) Pub Date : 2024-02-14 Anja K. Ehrmann, Anna K. Wronska, Perli Thomas, Erik A.F. de Hulster, Marijke A.H. Luttik, Marcel van den Broek, Clara Carqueija Cardoso, Jack T. Pronk, Jean-Marc Daran
Chemically defined media for cultivation of strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this
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KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states Metab. Eng. (IF 8.4) Pub Date : 2024-02-07 Mengqi Hu, Patrick F. Suthers, Costas D. Maranas
Large-scale kinetic models provide the computational means to dynamically link metabolic reaction fluxes to metabolite concentrations and enzyme levels while also conforming to substrate level regulation. However, the development of broadly applicable frameworks for efficiently and robustly parameterizing models remains a challenge. Challenges arise due to both the heterogeneity, paucity, and difficulty
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Engineering mammalian cell growth dynamics for biomanufacturing Metab. Eng. (IF 8.4) Pub Date : 2024-02-06 Mauro Torres, Dewi Mcconnaughie, Samia Akhtar, Claire E. Gaffney, Bruno Fievet, Catherine Ingham, Mark Stockdale, Alan J. Dickson
Precise control over mammalian cell growth dynamics poses a major challenge in biopharmaceutical manufacturing. Here, we present a multi-level cell engineering strategy for the tunable regulation of growth phases in mammalian cells. Initially, we engineered mammalian death phase by employing CRISPR/Cas9 to knockout pro-apoptotic proteins Bax and Bak, resulting in a substantial attenuation of apoptosis
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Metabolic engineering of Saccharomyces cerevisiae for de novo production of odd-numbered medium-chain fatty acids Metab. Eng. (IF 8.4) Pub Date : 2024-02-05 Genlai Dong, Ying Zhao, Wentao Ding, Shijie Xu, Qi Zhang, Huimin Zhao, Shuobo Shi
Odd-numbered fatty acids (FAs) have been widely used in nutrition, agriculture, and chemical industries. Recently, some studies showed that they could be produced from bacteria or yeast, but the products are almost exclusively odd-numbered long-chain FAs. Here we report the design and construction of two biosynthetic pathways in for production of odd-numbered medium-chain fatty acids (OMFAs) via ricinoleic
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A self-regulated network for dynamically balancing multiple precursors in complex biosynthetic pathways Metab. Eng. (IF 8.4) Pub Date : 2024-02-03 Yusong Zou, Jianli Zhang, Jian Wang, Xinyu Gong, Tian Jiang, Yajun Yan
Microbial synthesis has emerged as a promising and sustainable alternative to traditional chemical synthesis and plant extraction. However, the competition between synthetic pathways and central metabolic pathways for cellular resources may impair final production efficiency. Moreover, when the synthesis of target product requires multiple precursors from the same node, the conflicts of carbon flux
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LipidSIM: Inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, Markov modeling framework Metab. Eng. (IF 8.4) Pub Date : 2024-02-02 Chenguang Liang, Sue Murray, Yang Li, Richard Lee, Audrey Low, Shruti Sasaki, Austin W.T. Chiang, Wen-Jen Lin, Joel Mathews, Will Barnes, Nathan E. Lewis
Lipid metabolism is a complex and dynamic system involving numerous enzymes at the junction of multiple metabolic pathways. Disruption of these pathways leads to systematic dyslipidemia, a hallmark of many pathological developments, such as nonalcoholic steatohepatitis and diabetes. Recent advances in computational tools can provide insights into the dysregulation of lipid biosynthesis, but limitations
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Cross-regulation between proteome reallocation and metabolic flux redistribution governs bacterial growth transition kinetics Metab. Eng. (IF 8.4) Pub Date : 2024-02-02 Huili Yuan, Yang Bai, Xuefei Li, Xiongfei Fu
Bacteria need to adjust their metabolism and protein synthesis simultaneously to adapt to changing nutrient conditions. It’s still a grand challenge to predict how cells coordinate such adaptation due to the cross-regulation between the metabolic fluxes and the protein synthesis. Here we developed a dynamic Constrained Allocation Flux Balance Analysis method (dCAFBA), which integrates flux-controlled
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Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae Metab. Eng. (IF 8.4) Pub Date : 2024-02-02 Gustav Sjöberg, Alīna Reķēna, Matilda Fornstad, Petri-Jaan Lahtvee, Antonius J.A. van Maris
Enzyme-constrained genome-scale models (ecGEMs) have potential to predict phenotypes in a variety of conditions, such as growth rates or carbon sources. This study investigated if ecGEMs can guide metabolic engineering efforts to swap anaerobic redox-neutral ATP-providing pathways in yeast from alcoholic fermentation to equimolar co-production of 2,3-butanediol and glycerol. With proven pathways and
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Expression in CHO cells of a bacterial biosynthetic pathway producing a small non-ribosomal peptide aldehyde prevents proteolysis of recombinant proteins Metab. Eng. (IF 8.4) Pub Date : 2024-01-28 Violeta Guadarrama-Pérez, César Aguilar, Alberto Porras-Sanjuanico, Enrique Merino, Octavio T. Ramírez, Francisco Barona-Gómez, Laura A. Palomares
A significant problem during recombinant protein production is proteolysis. One of the most common preventive strategies is the addition of protease inhibitors, which has drawbacks, such as their short half-life and high cost, and their limited prevention of extracellular proteolysis. Actinomycetes produce the most commonly used inhibitors, which are non-ribosomal small aldehydic peptides. Previously
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Corrigendum to “Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells” [Metabol. Eng. 45 (2018) 149–157] Metab. Eng. (IF 8.4) Pub Date : 2024-01-19 Emanuel Gonçalves, Marco Sciacovelli, Ana S.H. Costa, Maxine Gia Binh Tran, Timothy Isaac Johnson, Daniel Machado, Christian Frezza, Julio Saez-Rodriguez
Abstract not available
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YaliCMulti and YaliHMulti: Stable, efficient multi-copy integration tools for engineering Yarrowia lipolytica Metab. Eng. (IF 8.4) Pub Date : 2024-01-14 Mengsu Liu, Junjun Wu, Mingyu Yue, Yang Ning, Xin Guan, Song Gao, Jingwen Zhou
Yarrowia lipolytica is widely used in biotechnology to produce recombinant proteins, food ingredients and diverse natural products. However, unstable expression of plasmids, difficult and time-consuming integration of single and low-copy-number plasmids hampers the construction of efficient production pathways and application to industrial production. Here, by exploiting sequence diversity in the long
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Consistent biosynthesis of D-glycerate from variable mixed substrates Metab. Eng. (IF 8.4) Pub Date : 2024-01-05 Cynthia Ni, Kristala L.J. Prather
The use of waste streams and other renewable feedstocks in microbial biosynthesis has long been a goal for metabolic engineers. Microbes can utilize the substrate mixtures found in waste streams, though they are more technically challenging to convert to useful products compared to the single substrates of standard practice. It is difficult to achieve consistent biosynthesis in the face of the temporally
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Enhanced poly-γ-glutamic acid synthesis in Corynebacterium glutamicum by reconstituting PgsBCA complex and fermentation optimization Metab. Eng. (IF 8.4) Pub Date : 2023-12-29 Guoqiang Xu, Jiyue Wang, Jiancheng Shen, Yaxin Zhu, Wanjing Liu, Yuhang Chen, Jian Zha, Xiaomei Zhang, Xiaojuan Zhang, Jinsong Shi, Mattheos A.G. Koffas, Zhenghong Xu
Previously, a novel Corynebacterium glutamicum strain for the de novo biosynthesis of tailored poly-γ-glutamic acid (γ-PGA) has been constructed by our group. The strain was based on the γ-PGA synthetase complex, PgsBCA, which is the only polyprotein complex responsible for γ-PGA synthesis in Bacillus spp. In the present study, PgsBCA was reconstituted and overexpressed in C. glutamicum to further
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Creating new-to-nature carbon fixation: A guide Metab. Eng. (IF 8.4) Pub Date : 2023-12-29 Helena Schulz-Mirbach, Beau Dronsella, Hai He, Tobias J. Erb
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Flux optimization using multiple promoters in Halomonas bluephagenesis as a model chassis of the next generation industrial biotechnology Metab. Eng. (IF 8.4) Pub Date : 2023-12-28 Yueyuan Ma, Jian-Wen Ye, Yina Lin, Xueqing Yi, Xuan Wang, Huan Wang, Ruiyan Huang, Fuqing Wu, Qiong Wu, Xu Liu, Guo-Qiang Chen
Predictability and robustness are challenges for bioproduction because of the unstable intracellular synthetic activities. With the deeper understanding of the gene expression process, fine-tuning has become a meaningful tool for biosynthesis optimization. This study characterized several gene expression elements and constructed a multiple inducible system that responds to ten different small chemical
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Engineering 5-hydroxymethylfurfural (HMF) oxidation in Pseudomonas boosts tolerance and accelerates 2,5-furandicarboxylic acid (FDCA) production Metab. Eng. (IF 8.4) Pub Date : 2023-12-26 Thorsten Lechtenberg, Benedikt Wynands, Nick Wierckx
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Selective microbial production of lacto-N-fucopentaose I in Escherichia coli using engineered α-1,2-fucosyltransferases Metab. Eng. (IF 8.4) Pub Date : 2023-12-24 Shun Endo, Tomotoshi Sugita, Sayaka Kamai, Kazuki Nakamura, Fuhito Yamazaki, Sotaro Sampei, Gustautas Snarskis, Audronė Valančiūtė, Masoud Kazemi, Irmantas Rokaitis, Kento Koketsu
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Inferring secretory and metabolic pathway activity from omic data with secCellFie Metab. Eng. (IF 8.4) Pub Date : 2023-12-23 Helen O. Masson, Mojtaba Samoudi, Caressa M. Robinson, Chih-Chung Kuo, Linus Weiss, Km Shams Ud Doha, Alex Campos, Vijay Tejwani, Hussain Dahodwala, Patrice Menard, Bjorn G. Voldborg, Bradley Robasky, Susan T. Sharfstein, Nathan E. Lewis
Understanding protein secretion has considerable importance in biotechnology and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway's activity remains challenging due
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Building a highly efficient Streptomyces super-chassis for secondary metabolite production by reprogramming naturally-evolved multifaceted shifts Metab. Eng. (IF 8.4) Pub Date : 2023-12-23 Shiwen Qiu, Bowen Yang, Zilong Li, Shanshan Li, Hao Yan, Zhenguo Xin, Jingfang Liu, Xuejin Zhao, Lixin Zhang, Wensheng Xiang, Weishan Wang
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Production of species-specific anthocyanins through an inducible system in plant hairy roots Metab. Eng. (IF 8.4) Pub Date : 2023-12-14 Jie Liu, Yuanxiu Zhao, Jingmeng Zhang, Yu Kong, Pan Liu, Yumin Fang, Mengying Cui, Tianlin Pei, Xin Zhong, Ping Xu, Wenqing Qiu, Dongfeng Yang, Cathie Martin, Qing Zhao
Anthocyanins are widely distributed pigments in flowering plants with red, purple or blue colours. Their properties in promoting heath make anthocyanins perfect natural colourants for food additives. However, anthocyanins with strong colour and stability at neutral pH, suitable as food colourants are relatively rare in nature. Acylation increases anthocyanin stability and confers bluer colour. In this
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Metabolic engineering of Halomonas bluephagenesis for production of five carbon molecular chemicals derived from L-lysine Metab. Eng. (IF 8.4) Pub Date : 2023-12-10 Fang Yang, Huan Wang, Cuihuan Zhao, Lizhan Zhang, Xu Liu, Helen Park, Yiping Yuan, Jian-Wen Ye, Qiong Wu, Guo-Qiang Chen
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Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus Metab. Eng. (IF 8.4) Pub Date : 2023-12-09 Julian Stegmüller, Marta Rodríguez Estévez, Wei Shu, Lars Gläser, Maksym Myronovskyi, Christian Rückert-Reed, Jörn Kalinowski, Andriy Luzhetskyy, Christoph Wittmann
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate
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Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold Metab. Eng. (IF 8.4) Pub Date : 2023-12-09 Niklas Berndt Thalén, Mona Moradi Barzadd, Magnus Lundqvist, Johanna Rodhe, Monica Andersson, Gholamreza Bidkhori, Dominik Possner, Chao Su, Joakim Nilsson, Peter Eisenhut, Magdalena Malm, Alice Karlsson, Jeanette Vestin, Johan Forsberg, Erik Nordling, Adil Mardinoglu, Anna-Luisa Volk, Anna Sandegren, Johan Rockberg
Rare diseases are, despite their name, collectively common and millions of people are affected daily of conditions where treatment often is unavailable. Sulfatases are a large family of activating enzymes related to several of these diseases. Heritable genetic variations in sulfatases may lead to impaired activity and a reduced macromolecular breakdown within the lysosome, with several severe and lethal
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Engineering Yarrowia lipolytica for sustainable ricinoleic acid production: A pathway to free fatty acid synthesis Metab. Eng. (IF 8.4) Pub Date : 2023-12-08 Kwanghyun Park, Ji-Sook Hahn
Ricinoleic acid (C18:1-OH, RA) is a valuable hydroxy fatty acid with versatile applications. The current industrial source of RA relies on the hydrolysis of castor bean oil. However, the coexistence of the toxic compound ricin and the unstable supply of this plant have led to an exploration of promising alternatives: generating RA in heterologous plants or microorganisms. In this study, we engineered
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Development of Corynebacterium glutamicum as a monoterpene production platform Metab. Eng. (IF 8.4) Pub Date : 2023-12-04 Bridget A. Luckie, Meera Kashyap, Allison N. Pearson, Yan Chen, Yuzhong Liu, Luis E. Valencia, Alexander Carrillo Romero, Graham A. Hudson, Xavier B. Tao, Bryan Wu, Christopher J. Petzold, Jay D. Keasling
Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however
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Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli Metab. Eng. (IF 8.4) Pub Date : 2023-12-02 Komal Sharma, Mohammad Rifqi Ghiffary, GaRyoung Lee, Hyun Uk Kim
Kynurenine pathway has a potential to convert L-tryptophan into multiple medicinal molecules. This study aims to explore the biosynthetic potential of kynurenine pathway for the efficient production of actinocin, an antitumor precursor selected as a proof-of-concept target molecule. Kynurenine pathway is first constructed in Escherichia coli by testing various combinations of biosynthetic genes from
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Enabling pathway design by multiplex experimentation and machine learning Metab. Eng. (IF 8.4) Pub Date : 2023-11-30 Aashutosh Girish Boob, Junyu Chen, Huimin Zhao
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error
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Engineering and evolution of the complete Reductive Glycine Pathway in Saccharomyces cerevisiae for formate and CO2 assimilation Metab. Eng. (IF 8.4) Pub Date : 2023-11-30 Viswanada R. Bysani, Ayesha S. Alam, Arren Bar-Even, Fabian Machens
Using captured CO2 and C1-feedstocks like formate and methanol derived from electrochemical activation of CO2 are key solutions for transforming industrial processes towards a circular carbon economy. Engineering formate and CO2-based growth in the biotechnologically relevant yeast Saccharomyces cerevisiae could boost the emergence of a formate-mediated circular bio-economy. This study adopts a growth-coupled
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Directed evolution of biomass intensive CHO cells by adaptation to sub-physiological temperature Metab. Eng. (IF 8.4) Pub Date : 2023-11-23 Katie L. Syddall, Alejandro Fernandez–Martell, Joseph F. Cartwright, Cristina N. Alexandru-Crivac, Adam Hodgson, Andrew J. Racher, Robert J. Young, David C. James
We report a simple and effective means to increase the biosynthetic capacity of host CHO cells. Lonza proprietary CHOK1SV® cells were evolved by serial sub-culture for over 150 generations at 32 °C. During this period the specific proliferation rate of hypothermic cells gradually recovered to become comparable to that of cells routinely maintained at 37 °C. Cold-adapted cell populations exhibited (1)
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Comparison of wild-type KT2440 and genome-reduced EM42 Pseudomonas putida strains for muconate production from aromatic compounds and glucose Metab. Eng. (IF 8.4) Pub Date : 2023-11-23 Caroline R. Amendola, William T. Cordell, Colin M. Kneucker, Caralyn J. Szostkiewicz, Morgan A. Ingraham, Michela Monninger, Rosemarie Wilton, Brian F. Pfleger, Davinia Salvachúa, Christopher W. Johnson, Gregg T. Beckham
Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has been previously conducted, resulting in P. putida strain EM42, which exhibited characteristics that could be advantageous for production strains. Here
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One-pot selective biosynthesis of Tyrian purple in Escherichia coli Metab. Eng. (IF 8.4) Pub Date : 2023-11-22 Feifei Li, Que Chen, Huaxiang Deng, Shumei Ye, Ruidong Chen, Jay D. Keasling, Xiaozhou Luo
Tyrian purple (6,6′-Dibromoindigo) is an ancient precious dye, which possesses remarkable properties as a biocompatible semiconductor material. Recently, biosynthesis has emerged as an alternative for the sustainable production of Tyrian purple from a natural substrate. However, the selectivity issue in enzymatic tryptophan (Trp) and bromotryptophan (6-Br-Trp) degradation was an obstacle for obtaining
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A smart RBS library and its prediction model for robust and accurate fine-tuning of gene expression in Bacillus species Metab. Eng. (IF 8.4) Pub Date : 2023-11-10 Xiaolan Rao, Dian Li, Zhaowei Su, Christopher T. Nomura, Shouwen Chen, Qin Wang
Bacillus species, such as Bacillus subtilis and Bacillus licheniformis, are important industrial bacteria. However, there is a lack of standardized and predictable genetic tools for convenient and reproducible assembly of genetic modules in Bacillus species to realize their full potential. In this study, we constructed a Ribosome Binding Site (RBS) library in B. licheniformis, which provides incremental
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Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942 Metab. Eng. (IF 8.4) Pub Date : 2023-11-02 María Santos-Merino, Jonathan K. Sakkos, Amit K. Singh, Daniel C. Ducat
Photosynthetic organisms need to balance the rate of photosynthesis with the utilization of photosynthetic products by downstream reactions. While such “source/sink” pathways are well-interrogated in plants, analogous regulatory systems are unknown or poorly studied in single-celled algal and cyanobacterial species. Towards the identification of energy/sugar sensors in cyanobacteria, we utilized an
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Metabolic impact of heterologous protein production in Pseudomonas putida: Insights into carbon and energy flux control Metab. Eng. (IF 8.4) Pub Date : 2023-11-02 Philippe Vogeleer, Pierre Millard, Ana-Sofia Ortega Arbulú, Katharina Pflüger-Grau, Andreas Kremling, Fabien Létisse
For engineered microorganisms, the production of heterologous proteins that are often useless to host cells represents a burden on resources, which have to be shared with normal cellular processes. Within a certain metabolic leeway, this competitive process has no impact on growth. However, once this leeway, or free capacity, is fully utilized, the extra load becomes a metabolic burden that inhibits
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Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism Metab. Eng. (IF 8.4) Pub Date : 2023-11-01 Melanie M. Callaghan, Eashant Thusoo, Bishal D. Sharma, Fitsum Getahun, David M. Stevenson, Costas Maranas, Daniel G. Olson, Lee R. Lynd, Daniel Amador-Noguez
Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13C and 2H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2H-labeled nutrient substrates faces limitations due to
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Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose Metab. Eng. (IF 8.4) Pub Date : 2023-10-30 Nicolas Huber, Edgar Alberto Alcalá-Orozco, Thomas Rexer, Udo Reichl, Steffen Klamt
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Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping Metab. Eng. (IF 8.4) Pub Date : 2023-10-26 Xiunan Yi, Blake J. Rasor, Nathalie Boadi, Katherine Louie, Trent R. Northen, Ashty S. Karim, Michael C. Jewett, Hal S. Alper
Building and optimizing biosynthetic pathways in engineered cells holds promise to address societal needs in energy, materials, and medicine, but it is often time-consuming. Cell-free synthetic biology has emerged as a powerful tool to accelerate design-build-test-learn cycles for pathway engineering with increased tolerance to toxic compounds. However, most cell-free pathway prototyping to date has
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Development of an efficient yeast platform for cannabigerolic acid biosynthesis Metab. Eng. (IF 8.4) Pub Date : 2023-10-26 Yunfeng Zhang, Jiulong Guo, PeiZhen Gao, Wei Yan, Junfeng Shen, Xiaozhou Luo, Jay D. Keasling
Cannabinoids are important therapeutical molecules for human ailments, cancer treatment, and SARS-CoV-2. The central cannabinoid, cannabigerolic acid (CBGA), is generated from geranyl pyrophosphate and olivetolic acid by Cannabis sativa prenyltransferase (CsPT4). Despite efforts to engineer microorganisms such as Saccharomyces cerevisiae (S. cerevisiae) for CBGA production, their titers remain suboptimal
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Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites Metab. Eng. (IF 8.4) Pub Date : 2023-10-19 Aude Geistodt-Kiener, Jean Chrisologue Totozafy, Géraldine Le Goff, Justine Vergne, Kaori Sakai, Jamal Ouazzani, Grégory Mouille, Muriel Viaud, Richard J. O'Connell, Jean-Félix Dallery
Transcriptomic studies have revealed that fungal pathogens of plants activate the expression of numerous biosynthetic gene clusters (BGC) exclusively when in presence of a living host plant. The identification and structural elucidation of the corresponding secondary metabolites remain challenging. The aim was to develop a polycistronic system for heterologous expression of fungal BGCs in Saccharomyces
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De novo biosynthesis of anticarcinogenic icariin in engineered yeast Metab. Eng. (IF 8.4) Pub Date : 2023-10-16 Ting An, Guangyuan Lin, Yang Liu, Lei Qin, Yuquan Xu, Xudong Feng, Chun Li
Icariin (ICA) has wide applications in nutraceuticals and medicine with strong anticancer activities. However, the structural complexity and low abundance in plants of ICA lead to the unsustainable and high-cost supply from chemical synthesis and plant extraction. Here, the whole biosynthesis pathway of ICA was elucidated, then was constructed in Saccharomyces cerevisiae, including a 13-step heterologous
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Metabolic engineering of oleaginous yeast in the lipogenic phase enhances production of nervonic acid Metab. Eng. (IF 8.4) Pub Date : 2023-10-10 Feixiang Liu, Zewei Lu, Tingting Lu, Manman Shi, Huimin Wang, Rong Wu, Jun Cao, Erzheng Su, Xiaoqiang Ma
Insufficient biosynthesis efficiency during the lipogenic phase can be a major obstacle to engineering oleaginous yeasts to overproduce very long-chain fatty acids (VLCFAs). Taking nervonic acid (NA, C24:1) as an example, we overcame the bottleneck to overproduce NA in an engineered Rhodosporidium toruloides by improving the biosynthesis of VLCFAs during the lipogenic phase. First, evaluating the catalytic