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Journal articles on the topic 'Rational Strain, Metabolic Engineering'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Tsouka, Sophia, Meric Ataman, Tuure Hameri, Ljubisa Miskovic, and Vassily Hatzimanikatis. "Constraint-based metabolic control analysis for rational strain engineering." Metabolic Engineering 66 (July 2021): 191–203. http://dx.doi.org/10.1016/j.ymben.2021.03.003.

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Dagariya, Sakshi, Janvi Bhatankar, Tikam Chand Dakal, Bhana Ram Gadi, and Paolo Giudici. "Metabolic and Evolutionary Engineering of Food Yeasts." Processes 13, no. 6 (2025): 1852. https://doi.org/10.3390/pr13061852.

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The yeast metabolic and evolutionary engineering, especially Saccharomyces cerevisiae, plays a significant role in the enhancement of its industrial applications in food, beverage, and biofuel production. This review integrates genetic engineering, systems biology, and evolutionary principles to optimize yeast performance, adaptability, and productivity. The key strategies which enable targeted genome modifications to improve substrate utilization, stress tolerance, and the biosynthesis of valuable metabolites such as flavor compounds, organic acids, vitamins, and antioxidants, including preci

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Freedman, Benjamin G., Parker W. Lee, and Ryan S. Senger. "Engineering the Metabolic Profile of Clostridium cellulolyticum with Genomic DNA Libraries." Fermentation 9, no. 7 (2023): 605. http://dx.doi.org/10.3390/fermentation9070605.

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Clostridium cellulolyticum H10 (ATCC 35319) has the ability to ferment cellulosic substrates into ethanol and weak acids. The growth and alcohol production rates of the wild-type organism are low and, therefore, targets of metabolic engineering. A genomic DNA expression library was produced by a novel application of degenerate oligonucleotide primed PCR (DOP-PCR) and was serially enriched in C. cellulolyticum grown on cellobiose in effort to produce fast-growing and productive strains. The DNA library produced from DOP-PCR contained gene-sized DNA fragments from the C. cellulolyticum genome an

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Burgardt, Arthur, Ludovic Pelosi, Mahmoud Hajj Chehade, Volker F. Wendisch, and Fabien Pierrel. "Rational Engineering of Non-Ubiquinone Containing Corynebacterium glutamicum for Enhanced Coenzyme Q10 Production." Metabolites 12, no. 5 (2022): 428. http://dx.doi.org/10.3390/metabo12050428.

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Coenzyme Q10 (CoQ10) is a lipid-soluble compound with important physiological functions and is sought after in the food and cosmetic industries owing to its antioxidant properties. In our previous proof of concept, we engineered for CoQ10 biosynthesis the industrially relevant Corynebacterium glutamicum, which does not naturally synthesize any CoQ. Here, liquid chromatography–mass spectrometry (LC–MS) analysis identified two metabolic bottlenecks in the CoQ10 production, i.e., low conversion of the intermediate 10-prenylphenol (10P-Ph) to CoQ10 and the accumulation of isoprenologs with prenyl

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Lentsch, Verena, Aurore Woller, Andrea Rocker, et al. "Vaccine-enhanced competition permits rational bacterial strain replacement in the gut." Science 388, no. 6742 (2025): 74–81. https://doi.org/10.1126/science.adp5011.

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Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied either prophylactically to prevent invasion of nontyphoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition.

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Gao, Zhenghao, Fengli Wu, Zhidan Zhang, et al. "Improvement of L-Tryptophan Production in Escherichia coli Using Biosensor-Based, High-Throughput Screening and Metabolic Engineering." Fermentation 11, no. 5 (2025): 267. https://doi.org/10.3390/fermentation11050267.

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The demand for L-tryptophan (L-Trp) has been rapidly increasing across various industries, including pharmaceuticals, food, and animal feed. However, traditional production methods have been unable to efficiently meet this growing demand. Hence, this study aimed to develop strategies for enhancing L-Trp production in Escherichia coli. Firstly, an L-Trp-producing strain was selected and subjected to atmospheric and room temperature plasma (ARTP) mutagenesis to generate a mutant library. This was followed by high-throughput screening using an L-Trp-specific riboswitch and a yellow fluorescent pr

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Zhu, Linghuan, Sha Xu, Youran Li, and Guiyang Shi. "Improvement of 2-phenylethanol production in Saccharomyces cerevisiae by evolutionary and rational metabolic engineering." PLOS ONE 16, no. 10 (2021): e0258180. http://dx.doi.org/10.1371/journal.pone.0258180.

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2-Phenylethanol (2-PE) is a valuable aromatic compound with favorable flavors and good properties, resulting in its widespread application in the cosmetic, food and medical industries. In this study, a mutant strain, AD032, was first obtained by adaptive evolution under 2-PE stress. Then, a fusion protein from the Ehrlich pathway, composed of tyrB from Escherichia coli, kdcA from Lactococcus lactis and ADH2 from Saccharomyces cerevisiae, was constructed and expressed. As a result, 3.14 g/L 2-PE was achieved using L-phenylalanine as a precursor. To further increase 2-PE production, L-glutamate

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Nevoigt, Elke. "Progress in Metabolic Engineering of Saccharomyces cerevisiae." Microbiology and Molecular Biology Reviews 72, no. 3 (2008): 379–412. http://dx.doi.org/10.1128/mmbr.00025-07.

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SUMMARY The traditional use of the yeast Saccharomyces cerevisiae in alcoholic fermentation has, over time, resulted in substantial accumulated knowledge concerning genetics, physiology, and biochemistry as well as genetic engineering and fermentation technologies. S. cerevisiae has become a platform organism for developing metabolic engineering strategies, methods, and tools. The current review discusses the relevance of several engineering strategies, such as rational and inverse metabolic engineering, evolutionary engineering, and global transcription machinery engineering, in yeast strain

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Natarajan, Aravind, Thapakorn Jaroentomeechai, Mingji Li, Cameron J. Glasscock, and Matthew P. DeLisa. "Metabolic engineering of glycoprotein biosynthesis in bacteria." Emerging Topics in Life Sciences 2, no. 3 (2018): 419–32. http://dx.doi.org/10.1042/etls20180004.

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The demonstration more than a decade ago that glycoproteins could be produced in Escherichia coli cells equipped with the N-linked protein glycosylation machinery from Campylobacter jejuni opened the door to using simple bacteria for the expression and engineering of complex glycoproteins. Since that time, metabolic engineering has played an increasingly important role in developing and optimizing microbial cell glyco-factories for the production of diverse glycoproteins and other glycoconjugates. It is becoming clear that future progress in creating efficient glycoprotein expression platforms

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Huang, Wei, Yongheng Liu, Xiaomei Ma, Cilang Ma, Yuting Jiang, and Jianyu Su. "Rational Design for the Complete Synthesis of Stevioside in Saccharomyces cerevisiae." Microorganisms 12, no. 6 (2024): 1125. http://dx.doi.org/10.3390/microorganisms12061125.

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Stevioside is a secondary metabolite of diterpenoid glycoside production in plants. It has been used as a natural sweetener in various foods because of its high sweetness and low-calorie content. In this study, we constructed a Saccharomyces cerevisiae strain for the complete synthesis of stevioside using a metabolic engineering strategy. Firstly, the synthesis pathway of steviol was modularly constructed in S. cerevisiae BY4742, and the precursor pathway was strengthened. The yield of steviol was used as an indicator to investigate the expression effect of different sources of diterpene synth

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Zhang, Xiaomei, Zhenhang Sun, Jinyu Bian, et al. "Rational Metabolic Engineering Combined with Biosensor-Mediated Adaptive Laboratory Evolution for l-Cysteine Overproduction from Glycerol in Escherichia coli." Fermentation 8, no. 7 (2022): 299. http://dx.doi.org/10.3390/fermentation8070299.

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l-Cysteine is an important sulfur-containing amino acid with numerous applications in the pharmaceutical and cosmetic industries. The microbial production of l-cysteine has received substantial attention, and the supply of the precursor l-serine is important in l-cysteine biosynthesis. In this study, to achieve l-cysteine overproduction, we first increased l-serine production by deleting genes involved in the pathway of l-serine degradation to glycine (serine hydroxymethyl transferase, SHMT, encoded by glyA genes) in strain 4W (with l-serine titer of 1.1 g/L), thus resulting in strain 4WG with

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Tafur Rangel, Albert E., Abel García Oviedo, Freddy Cabrera Mojica, Jorge M. Gómez, and Andrés Fernando Gónzalez Barrios. "Development of an integrating systems metabolic engineering and bioprocess modeling approach for rational strain improvement." Biochemical Engineering Journal 178 (January 2022): 108268. http://dx.doi.org/10.1016/j.bej.2021.108268.

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13

Iacometti, Camillo, Katharina Marx, Maria Hönick, et al. "Activating Silent Glycolysis Bypasses in Escherichia coli." BioDesign Research 2022 (May 12, 2022): 1–17. http://dx.doi.org/10.34133/2022/9859643.

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All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes p

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Jeong, Sun-Wook, Jun-Ho Kim, Ji-Woong Kim, Chae Yeon Kim, Su Young Kim, and Yong Jun Choi. "Metabolic Engineering of Extremophilic Bacterium Deinococcus radiodurans for the Production of the Novel Carotenoid Deinoxanthin." Microorganisms 9, no. 1 (2020): 44. http://dx.doi.org/10.3390/microorganisms9010044.

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Deinoxanthin, a xanthophyll derived from Deinococcus species, is a unique organic compound that provides greater antioxidant effects compared to other carotenoids due to its superior scavenging activity against singlet oxygen and hydrogen peroxide. Therefore, it has attracted significant attention as a next-generation organic compound that has great potential as a natural ingredient in a food supplements. Although the microbial identification of deinoxanthin has been identified, mass production has not yet been achieved. Here, we report, for the first time, the development of an engineered ext

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Fuchino, Katsuya, Uldis Kalnenieks, Reinis Rutkis, Mara Grube, and Per Bruheim. "Metabolic Profiling of Glucose-Fed Metabolically Active Resting Zymomonas mobilis Strains." Metabolites 10, no. 3 (2020): 81. http://dx.doi.org/10.3390/metabo10030081.

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Zymomonas mobilis is the most efficient bacterial ethanol producer and its physiology is potentially applicable to industrial-scale bioethanol production. However, compared to other industrially important microorganisms, the Z. mobilis metabolome and adaptation to various nutritional and genetic perturbations have been poorly characterized. For rational metabolic engineering, it is essential to understand how central metabolism and intracellular redox balance are maintained in Z. mobilis under various conditions. In this study, we applied quantitative mass spectrometry-based metabolomics to ex

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Arora, Neha, Hong-Wei Yen, and George P. Philippidis. "Harnessing the Power of Mutagenesis and Adaptive Laboratory Evolution for High Lipid Production by Oleaginous Microalgae and Yeasts." Sustainability 12, no. 12 (2020): 5125. http://dx.doi.org/10.3390/su12125125.

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Oleaginous microalgae and yeasts represent promising candidates for large-scale production of lipids, which can be utilized for production of drop-in biofuels, nutraceuticals, pigments, and cosmetics. However, low lipid productivity and costly downstream processing continue to hamper the commercial deployment of oleaginous microorganisms. Strain improvement can play an essential role in the development of such industrial microorganisms by increasing lipid production and hence reducing production costs. The main means of strain improvement are random mutagenesis, adaptive laboratory evolution (

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17

Stovicek, Vratislav, Laura Dato, Henrik Almqvist, et al. "Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate." Biotechnology for Biofuels and Bioproducts 15, no. 1 (2022): 22. https://doi.org/10.1186/s13068-022-02121-1.

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<strong>Background: </strong>Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars—in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnolog

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Zhang, Chi, Zhongjie Yan, Xiufang Li, Junming Wang, Xidong Ren, and Xinli Liu. "Comprehensive Analysis of Catalytic Characteristics and Molecular Mechanisms in Mutant Trametes versicolor Strains with Enhanced Laccase Activities." Fermentation 9, no. 12 (2023): 995. http://dx.doi.org/10.3390/fermentation9120995.

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The commercial potential of Trametes versicolor laccases in the degradation of various persistent contaminants is significant. Despite numerous attempts through rational metabolic engineering to enhance the properties of laccases, the outcomes have proven unsatisfactory for practical implementation. The present study successfully generated two novel mutants, namely, TA-04 and TA-15, derived from Trametes versicolor ATCC20869, utilizing atmospheric and room temperature plasma (ARTP). The laccase activities of TA-04 and TA-15 showed a significant increase to 136.507 ± 4.827 U/mg DCW and 153.804

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Hofer, Katharina, Lynn S. Schwardmann, Jung-Won Youn, Volker F. Wendisch, and Ralf Takors. "Single Mutation in iolT1 in ptsG-Deficient Corynebacterium glutamicum Enables Growth Boost in Xylose-Containing Media." Microorganisms 13, no. 7 (2025): 1606. https://doi.org/10.3390/microorganisms13071606.

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Efficient co-utilization of glucose and xylose from lignocellulosic biomass remains a critical bottleneck limiting the viability of sustainable biorefineries. While Corynebacterium glutamicum has emerged as a promising industrial host due to its robustness, further improvements in mixed-sugar co-utilization are needed. Here, we demonstrate how a single amino acid substitution can dramatically transform cellular sugar transport capacity. By combining rational strain engineering with continuous adaptive laboratory evolution, we evolved a ptsG-deficient C. glutamicum strain in glucose–xylose mixt

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Xu, Feng, Xiang Ke, Ming Hong, et al. "Exploring the metabolic fate of propanol in industrial erythromycin-producing strain via 13C labeling experiments and enhancement of erythromycin production by rational metabolic engineering of Saccharopolyspora erythraea." Biochemical and Biophysical Research Communications 542 (February 2021): 73–79. http://dx.doi.org/10.1016/j.bbrc.2021.01.024.

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Topaloğlu, Alican, Ömer Esen, Burcu Turanlı-Yıldız, Mevlüt Arslan, and Zeynep Petek Çakar. "From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications." Journal of Fungi 9, no. 10 (2023): 984. http://dx.doi.org/10.3390/jof9100984.

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Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned

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Wang, Qingzhao, Mark S. Ou, Y. Kim, L. O. Ingram, and K. T. Shanmugam. "Metabolic Flux Control at the Pyruvate Node in an Anaerobic Escherichia coli Strain with an Active Pyruvate Dehydrogenase." Applied and Environmental Microbiology 76, no. 7 (2010): 2107–14. http://dx.doi.org/10.1128/aem.02545-09.

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ABSTRACT During anaerobic growth of Escherichia coli, pyruvate formate-lyase (PFL) and lactate dehydrogenase (LDH) channel pyruvate toward a mixture of fermentation products. We have introduced a third branch at the pyruvate node in a mutant of E. coli with a mutation in pyruvate dehydrogenase (PDH*) that renders the enzyme less sensitive to inhibition by NADH. The key starting enzymes of the three branches at the pyruvate node in such a mutant, PDH*, PFL, and LDH, have different metabolic potentials and kinetic properties. In such a mutant (strain QZ2), pyruvate flux through LDH was about 30%

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Dwijayanti, Ari, Marko Storch, Guy-Bart Stan, and Geoff S. Baldwin. "A modular RNA interference system for multiplexed gene regulation." Nucleic Acids Research 50, no. 3 (2022): 1783–93. http://dx.doi.org/10.1093/nar/gkab1301.

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Abstract The rational design and realisation of simple-to-use genetic control elements that are modular, orthogonal and robust is essential to the construction of predictable and reliable biological systems of increasing complexity. To this effect, we introduce modular Artificial RNA interference (mARi), a rational, modular and extensible design framework that enables robust, portable and multiplexed post-transcriptional regulation of gene expression in Escherichia coli. The regulatory function of mARi was characterised in a range of relevant genetic contexts, demonstrating its independence fr

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Miskovic, Ljubisa, Susanne Alff-Tuomala, Keng Cher Soh, et al. "A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models." Biotechnology for Biofuels 10, no. 1 (2017): 166. https://doi.org/10.1186/s13068-017-0838-5.

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<strong>Background: </strong>Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic models. These models can help us to uncover new insights into cellular physiology and also to assist in the rational design of bioreactor or fermentation processes. Optimization and Risk Analysis of Complex Living Entities (ORACLE) framework for the construction of large-scale kinetic models can be used as guidanc

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Sheremetieva, M. E., K. E. Anufriev, T. M. Khlebodarova, N. A. Kolchanov, and A. S. Yanenko. "Rational metabolic engineering of <i>Corynebacterium glutamicum</i> to create a producer of L-valine." Vavilov Journal of Genetics and Breeding 26, no. 8 (2023): 743–57. http://dx.doi.org/10.18699/vjgb-22-90.

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L-Valine is one of the nine amino acids that cannot be synthesized de novo by higher organisms and must come from food. This amino acid not only serves as a building block for proteins, but also regulates protein and energy metabolism and participates in neurotransmission. L-Valine is used in the food and pharmaceutical industries, medicine and cosmetics, but primarily as an animal feed additive. Adding L-valine to feed, alone or mixed with other essential amino acids, allows for feeds with lower crude protein content, increases the quality and quantity of pig meat and broiler chicken meat, as

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Pyne, Michael E., Stanislav Sokolenko, Xuejia Liu, et al. "Disruption of the Reductive 1,3-Propanediol Pathway Triggers Production of 1,2-Propanediol for Sustained Glycerol Fermentation by Clostridium pasteurianum." Applied and Environmental Microbiology 82, no. 17 (2016): 5375–88. http://dx.doi.org/10.1128/aem.01354-16.

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ABSTRACTCrude glycerol, the major by-product of biodiesel production, is an attractive bioprocessing feedstock owing to its abundance, low cost, and high degree of reduction. In line with the advent of the biodiesel industry,Clostridium pasteurianumhas gained prominence as a result of its unique capacity to convert waste glycerol inton-butanol, a high-energy biofuel. However, no efforts have been directed at abolishing the production of 1,3-propanediol (1,3-PDO), the chief competing product ofC. pasteurianumglycerol fermentation. Here, we report rational metabolic engineering ofC. pasteurianum

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Choi, Bo Hyun, Hyun Joon Kang, Sun Chang Kim, and Pyung Cheon Lee. "Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae." Microorganisms 10, no. 3 (2022): 650. http://dx.doi.org/10.3390/microorganisms10030650.

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Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Sacch

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Paramasivan, Kalaivani, Aneesha Abdulla, Nabarupa Gupta, and Sarma Mutturi. "In silico target-based strain engineering of Saccharomyces cerevisiae for terpene precursor improvement." Integrative Biology 14, no. 2 (2022): 25–36. http://dx.doi.org/10.1093/intbio/zyac003.

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Abstract Systems-based metabolic engineering enables cells to enhance product formation by predicting gene knockout and overexpression targets using modeling tools. FOCuS, a novel metaheuristic tool, was used to predict flux improvement targets in terpenoid pathway using the genome-scale model of Saccharomyces cerevisiae, iMM904. Some of the key knockout target predicted includes LYS1, GAP1, AAT1, AAT2, TH17, KGD-m, MET14, PDC1 and ACO1. It was also observed that the knockout reactions belonged either to fatty acid biosynthesis, amino acid synthesis pathways or nucleotide biosynthesis pathways

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Pyne, Michael, Murray Moo-Young, Duane Chung, and C. Chou. "Antisense-RNA-Mediated Gene Downregulation in Clostridium pasteurianum." Fermentation 1, no. 1 (2015): 113–26. http://dx.doi.org/10.3390/fermentation1010113.

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Clostridium pasteurianum is receiving growing attention for its unique metabolic properties, particularly its ability to convert waste glycerol and glycerol-rich byproducts into butanol, a prospective biofuel. Genetic tool development and whole genome sequencing have recently been investigated to advance the genetic tractability of this potential industrial host. Nevertheless, methodologies for tuning gene expression through plasmid-borne expression and chromosomal gene downregulation are still absent. Here we demonstrate plasmid-borne heterologous gene expression and gene knockdown using anti

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Deeba, Farha, Kukkala Kiran Kumar, Girish H. Rajacharya, and Naseem A. Gaur. "Metabolomic Profiling Revealed Diversion of Cytidinediphosphate-Diacylglycerol and Glycerol Pathway towards Denovo Triacylglycerol Synthesis in Rhodosporidium toruloides." Journal of Fungi 7, no. 11 (2021): 967. http://dx.doi.org/10.3390/jof7110967.

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Oleaginous yeast Rhodosporidium toruloides has great biotechnological potential and scientific interest, yet the molecular rationale of its cellular behavior to carbon and nitrogen ratios with concurrent lipid agglomeration remains elusive. Here, metabolomics adaptations of the R. toruloides in response to varying glucose and nitrogen concentrations have been investigated. In preliminary screening we found that 5% glucose (w/v) was optimal for further analysis in Rhodosporidium toruloides 3641. Hereafter, the effect of complementation to increase lipid agglomeration was evaluated with differen

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Neves, Rui P. P., Bruno Araújo, Maria J. Ramos, and Pedro A. Fernandes. "Feedback Inhibition of DszC, a Crucial Enzyme for Crude Oil Biodessulfurization." Catalysts 13, no. 4 (2023): 736. http://dx.doi.org/10.3390/catal13040736.

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The Rhodococcus erythropolis (strain IGTS8) bacterium has a tremendous industrial interest as it can remove sulfur from crude oil through its four-enzyme (DszA-D) 4S metabolic pathway. DszC is one of the rate-limiting enzymes of the pathway and the one that most suffers from feedback inhibition. We have combined molecular docking and molecular dynamics simulations to identify binding sites through which two products of the 4S pathway, 2-hydroxybiphenyl and 2′-hydroxybiphenyl-2-sulfinate, induce DszC feedback inhibition. We have identified four potential binding sites: two adjacent binding site

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Huang, Mingtao, Yunpeng Bai, Staffan L. Sjostrom, et al. "Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast." Proceedings of the National Academy of Sciences 112, no. 34 (2015): E4689—E4696. http://dx.doi.org/10.1073/pnas.1506460112.

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There is an increasing demand for biotech-based production of recombinant proteins for use as pharmaceuticals in the food and feed industry and in industrial applications. Yeast Saccharomyces cerevisiae is among preferred cell factories for recombinant protein production, and there is increasing interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by U

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Pan, Guohui, Zhengren Xu, Zhikai Guo, et al. "Discovery of the leinamycin family of natural products by mining actinobacterial genomes." Proceedings of the National Academy of Sciences 114, no. 52 (2017): E11131—E11140. http://dx.doi.org/10.1073/pnas.1716245115.

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Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based

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Darbani, Behrooz. "Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44." International Journal of Molecular Sciences 22, no. 11 (2021): 5669. http://dx.doi.org/10.3390/ijms22115669.

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Gene clusters are becoming promising tools for gene identification. The study reveals the purposive genomic distribution of genes toward higher inheritance rates of intact metabolic pathways/phenotypes and, thereby, higher fitness. The co-localization of co-expressed, co-interacting, and functionally related genes was found as genome-wide trends in humans, mouse, golden eagle, rice fish, Drosophila, peanut, and Arabidopsis. As anticipated, the analyses verified the co-segregation of co-localized events. A negative correlation was notable between the likelihood of co-localization events and the

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Wiedemann, Beate, and Eckhard Boles. "Codon-Optimized Bacterial Genes Improve l-Arabinose Fermentation in Recombinant Saccharomyces cerevisiae." Applied and Environmental Microbiology 74, no. 7 (2008): 2043–50. http://dx.doi.org/10.1128/aem.02395-07.

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ABSTRACT Bioethanol produced by microbial fermentations of plant biomass hydrolysates consisting of hexose and pentose mixtures is an excellent alternative to fossil transportation fuels. However, the yeast Saccharomyces cerevisiae, commonly used in bioethanol production, can utilize pentose sugars like l-arabinose or d-xylose only after heterologous expression of corresponding metabolic pathways from other organisms. Here we report the improvement of a bacterial l-arabinose utilization pathway consisting of l-arabinose isomerase from Bacillus subtilis and l-ribulokinase and l-ribulose-5-P 4-e

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Carlson, Ross, David Fell, and Friedrich Srienc. "Metabolic pathway analysis of a recombinant yeast for rational strain development." Biotechnology and Bioengineering 79, no. 2 (2002): 121–34. http://dx.doi.org/10.1002/bit.10305.

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Ye, Changchuan, Yuting Yang, Xi Chen, et al. "Metabolic engineering of Escherichia coli BW25113 for the production of 5-Aminolevulinic Acid based on CRISPR/Cas9 mediated gene knockout and metabolic pathway modification." Journal of Biological Engineering 16, no. 1 (2022). http://dx.doi.org/10.1186/s13036-022-00307-7.

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Abstract Background 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields. In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement based on known regulatory and metabolic information and CRISPR/Cas9 mediated gene knockout. Results A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via the C5 pathway was applied herein. The rational metabolic engineering by gene knockouts significantly improved ALA production from 662.3 to 1601.

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Yang, Yuting, Yuhong Zou, Xi Chen, et al. "Metabolic engineering of Escherichia coli for the production of 5-aminolevulinic acid based on combined metabolic pathway modification and reporter-guided mutant selection (RGMS)." Biotechnology for Biofuels and Bioproducts 17, no. 1 (2024). http://dx.doi.org/10.1186/s13068-024-02530-4.

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Abstract Background 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields such as medicine, nutrition and agriculture. Metabolic engineering is an efficient strategy to improve microbial production of 5-ALA. Results In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement. A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via both C4 and C5 pathways was applied herein. The expression of a modified hemARS gene and rational metab

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Yang, Qiang, Dongbo Cai, Wenshou Chen, Huiying Chen, and Wei Luo. "Combined metabolic analyses for the biosynthesis pathway of l-threonine in Escherichia coli." Frontiers in Bioengineering and Biotechnology 10 (September 9, 2022). http://dx.doi.org/10.3389/fbioe.2022.1010931.

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Currently, industrial production of l-threonine (Thr) is based on direct fermentation with microorganisms such as Escherichia coli, which has the characteristics of low cost and high productivity. In order to elucidate the key metabolic features of the synthesis pathway of Thr in E. coli to provide clues for metabolic regulation or engineering of the strain, this study was carried out on an l-threonine over-producing strain, in terms of analyses of metabolic flux, enzyme control and metabonomics. Since environmental disturbance and genetic modification are considered to be two important method

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Herman, Nicolaus A., Jeffrey Li, Ripika Bedi, et al. "Development of a High-Efficiency Transformation Method and Implementation of Rational Metabolic Engineering for the Industrial Butanol Hyperproducer Clostridium saccharoperbutylacetonicum Strain N1-4." Applied and Environmental Microbiology 83, no. 2 (2016). http://dx.doi.org/10.1128/aem.02942-16.

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ABSTRACT While a majority of academic studies concerning acetone, butanol, and ethanol (ABE) production by Clostridium have focused on Clostridium acetobutylicum, other members of this genus have proven to be effective industrial workhorses despite the inability to perform genetic manipulations on many of these strains. To further improve the industrial performance of these strains in areas such as substrate usage, solvent production, and end product versatility, transformation methods and genetic tools are needed to overcome the genetic intractability displayed by these species. In this study

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Xiao, Yubei, Xuemei Tan, Qiaoning He та Shihui Yang. "Systematic metabolic engineering of Zymomonas mobilis for β-farnesene production". Frontiers in Bioengineering and Biotechnology 12 (17 травня 2024). http://dx.doi.org/10.3389/fbioe.2024.1392556.

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Zymomonas mobilis is an ethanologenic bacterium that can produce hopanoids using farnesyl pyrophosphate (FPP), which can be used as the precursor by β-farnesene synthase for β-farnesene production. To explore the possibility and bottlenecks of developing Z. mobilis for β-farnesene production, five heterologous β-farnesene synthases were selected and screened, and AaBFS from Artemisia annua had the highest β-farnesene titer. Recombinant strains with AaBFS driven by the strong constitutive promoter Pgap (Pgap–AaBFS) doubled its β-farnesene production to 25.73 ± 0.31 mg/L compared to the recombin

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Hao, Yanan, Xuewei Pan, Guomin Li, et al. "Construction of a plasmid-free l-leucine overproducing Escherichia coli strain through reprogramming of the metabolic flux." Biotechnology for Biofuels and Bioproducts 16, no. 1 (2023). http://dx.doi.org/10.1186/s13068-023-02397-x.

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Abstract Background l-Leucine is a high-value amino acid with promising applications in the medicine and feed industries. However, the complex metabolic network and intracellular redox imbalance in fermentative microbes limit their efficient biosynthesis of l-leucine. Results In this study, we applied rational metabolic engineering and a dynamic regulation strategy to construct a plasmid-free, non-auxotrophic Escherichia coli strain that overproduces l-leucine. First, the l-leucine biosynthesis pathway was strengthened through multi-step rational metabolic engineering. Then, a cooperative cofa

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Lo, Jonathan, Chao Wu, Jonathan R. Humphreys, et al. "Thermodynamic and Kinetic Modeling Directs Pathway Optimization for Isopropanol Production in a Gas-Fermenting Bacterium." mSystems, March 27, 2023. http://dx.doi.org/10.1128/msystems.01274-22.

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Highly efficient bioproduction from gaseous substrates (e.g., hydrogen and carbon oxides) will require systematic optimization of the host microbes. To date, the rational redesign of gas-fermenting bacteria is still in its infancy, due in part to the lack of quantitative and precise metabolic knowledge that can direct strain engineering.

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Rajacharya, Girish H., Ashima Sharma, and Syed Shams Yazdani. "Proteomics and metabolic burden analysis to understand the impact of recombinant protein production in E. coli." Scientific Reports 14, no. 1 (2024). http://dx.doi.org/10.1038/s41598-024-63148-y.

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AbstractThe impact of recombinant protein production (RPP) on host cells and the metabolic burden associated with it undermine the efficiency of the production system. This study utilized proteomics to investigate the dynamics of parent and recombinant cells induced at different time points for RPP. The results revealed significant changes in both transcriptional and translational machinery that may have impacted the metabolic burden, growth rate of the culture and the RPP. The timing of protein synthesis induction also played a critical role in the fate of the recombinant protein within the h

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Li, Zhongcai, Qian Liu, Jiahui Sun, et al. "Multivariate modular metabolic engineering for enhanced l-methionine biosynthesis in Escherichia coli." Biotechnology for Biofuels and Bioproducts 16, no. 1 (2023). http://dx.doi.org/10.1186/s13068-023-02347-7.

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Abstract Background l-Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and strictly regulated biosynthesis, the development of microbial strains for high-level l-methionine production has remained challenging in recent years. Results By strengthening the l-methionine terminal synthetic module via site-directed mutation of l-homoserine O-succinyltransferase (MetA) and overexpression of metAfbr, metC, and yjeH, l-methionine production was increased to 1.93 g/L in shake flask fermentation. Deletion of the pykA and pyk

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Wan, Yupeng, Hongchen Liu, Mo Xian, and Wei Huang. "Biosynthesis and metabolic engineering of 1-hydroxyphenazine in Pseudomonas chlororaphis H18." Microbial Cell Factories 20, no. 1 (2021). http://dx.doi.org/10.1186/s12934-021-01731-y.

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Abstract Background 1-Hydroxyphenazine (1-OH-PHZ) is a phenazine microbial metabolite with broad-spectrum antibacterial activities against a lot of plant pathogens. However, its use is hampered by the low yield all along. Metabolic engineering of microorganisms is an increasingly powerful method for the production of valuable organisms at high levels. Pseudomonas chlororaphis is recognized as a safe and effective plant rhizosphere growth-promoting bacterium, and faster growth rate using glycerol or glucose as a renewable carbon source. Therefore, Pseudomonas chlororaphis is particularly suitab

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Li, Zhenxin, Songbai Yang, Zhengyu Zhang, et al. "Enhancement of acarbose production by genetic engineering and fed-batch fermentation strategy in Actinoplanes sp. SIPI12-34." Microbial Cell Factories 21, no. 1 (2022). http://dx.doi.org/10.1186/s12934-022-01969-0.

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Abstract Background Acarbose, as an alpha-glucosidase inhibitor, is widely used clinically to treat type II diabetes. In its industrial production, Actinoplanes sp. SE50/110 is used as the production strain. Lack of research on its regulatory mechanisms and unexplored gene targets are major obstacles to rational strain design. Here, transcriptome sequencing was applied to uncover more gene targets and rational genetic engineering was performed to increase acarbose production. Results In this study, with the help of transcriptome information, a TetR family regulator (TetR1) was identified and c

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Zhu, Zhijian, Manyu Zhang, Dandan Liu, et al. "Development of the thermophilic fungus Myceliophthora thermophila into glucoamylase hyperproduction system via the metabolic engineering using improved AsCas12a variants." Microbial Cell Factories 22, no. 1 (2023). http://dx.doi.org/10.1186/s12934-023-02149-4.

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Abstract Background Glucoamylase is an important enzyme for starch saccharification in the food and biofuel industries and mainly produced from mesophilic fungi such as Aspergillus and Rhizopus species. Enzymes produced from thermophilic fungi can save the fermentation energy and reduce costs as compared to the fermentation system using mesophiles. Thermophilic fungus Myceliophthora thermophila is industrially deployed fungus to produce enzymes and biobased chemicals from biomass during optimal growth at 45 °C. This study aimed to construct the M. thermophila platform for glucoamylase hyper-pr

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Blázquez, Blas, and Juan Nogales. "Rational Design Assisted by Evolutionary Engineering Allows (De)Construction and Optimization of Complex Phenotypes in Pseudomonas putida KT2440." Microbial Biotechnology 18, no. 3 (2025). https://doi.org/10.1111/1751-7915.70132.

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ABSTRACTBeyond the rational construction of genetic determinants to encode target functions, complex phenotype engineering requires the contextualisation of their expression within the metabolic and genetic background of the host strain. Furthermore, wherever metabolic complexity is involved, phenotype engineering demands standard, reliable, plug‐and‐play tools. We introduce GENIO (GENome Integration and fitness Optimization platform for Pseudomonas putida), a framework to optimise genetic circuit performance by means of (i) chromosome‐location‐based differential gene expression and (ii) subse

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Huang, Jia-jun, Tao Wei, Zhi-wei Ye, et al. "Microbial Cell Factory of Baccatin III Preparation in Escherichia coli by Increasing DBAT Thermostability and in vivo Acetyl-CoA Supply." Frontiers in Microbiology 12 (January 12, 2022). http://dx.doi.org/10.3389/fmicb.2021.803490.

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Given the rapid development of genome mining in this decade, the substrate channel of paclitaxel might be identified in the near future. A robust microbial cell factory with gene dbat, encoding a key rate-limiting enzyme 10-deacetylbaccatin III-10-O-transferase (DBAT) in paclitaxel biosynthesis to synthesize the precursor baccatin III, will lay out a promising foundation for paclitaxel de novo synthesis. Here, we integrated gene dbat into the wild-type Escherichia coli BW25113 to construct strain BWD01. Yet, it was relatively unstable in baccatin III synthesis. Mutant gene dbatS189V with impro

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