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Metabolic Engineering

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https://www.readbyqxmd.com/read/29229581/balancing-cellular-redox-metabolism-in-microbial-electrosynthesis-and-electro-fermentation-a-chance-for-metabolic-engineering
#1
REVIEW
Frauke Kracke, Bin Lai, Shiqin Yu, Jens O Krömer
More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimising microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes...
December 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29203223/expression-of-heterologous-non-oxidative-pentose-phosphate-pathway-from-bacillus-methanolicus-and-phosphoglucose-isomerase-deletion-improves-methanol-assimilation-and-metabolite-production-by-a-synthetic-escherichia-coli-methylotroph
#2
R Kyle Bennett, Jacqueline E Gonzalez, W Brian Whitaker, Maciek R Antoniewicz, Eleftherios T Papoutsakis
Synthetic methylotrophy aims to develop non-native methylotrophic microorganisms to utilize methane or methanol to produce chemicals and biofuels. We report two complimentary strategies to further engineer a previously engineered methylotrophic E. coli strain for improved methanol utilization. First, we demonstrate improved methanol assimilation in the presence of small amounts of yeast extract by expressing the non-oxidative pentose phosphate pathway (PPP) from Bacillus methanolicus. Second, we demonstrate improved co-utilization of methanol and glucose by deleting the phosphoglucose isomerase gene (pgi), which rerouted glucose carbon flux through the oxidative PPP...
December 5, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29203222/methanol-assimilation-in-escherichia-coli-is-improved-by-co-utilization-of-threonine-and-deletion-of-leucine-responsive-regulatory-protein
#3
Jacqueline E Gonzalez, R Kyle Bennett, E Terry Papoutsakis, Maciek R Antoniewicz
Methane, the main component of natural gas, can be used to produce methanol which can be further converted to other valuable products. There is increasing interest in using biological systems for the production of fuels and chemicals from methanol, termed methylotrophy. In this work, we have examined methanol assimilation metabolism in a synthetic methylotrophic E. coli strain. Specifically, we applied 13C-tracers and evaluated 25 different co-substrates for methanol assimilation, including amino acids, sugars and organic acids...
December 2, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29199104/reverse-engineering-the-cancer-metabolic-network-using-flux-analysis-to-understand-drivers-of-human-disease
#4
REVIEW
Mehmet G Badur, Christian M Metallo
Metabolic dysfunction has reemerged as an essential hallmark of tumorigenesis, and metabolic phenotypes are increasingly being integrated into pre-clinical models of disease. The complexity of these metabolic networks requires systems-level interrogation, and metabolic flux analysis (MFA) with stable isotope tracing present a suitable conceptual framework for such systems. Here we review efforts to elucidate mechanisms through which metabolism influences tumor growth and survival, with an emphasis on applications using stable isotope tracing and MFA...
November 30, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29199103/diversion-of-the-long-chain-acyl-acp-pool-in-synechocystis-to-fatty-alcohols-through-crispri-repression-of-the-essential-phosphate-acyltransferase-plsx
#5
Danuta Kaczmarzyk, Ivana Cengic, Lun Yao, Elton P Hudson
Fatty alcohol production in Synechocystis sp. PCC 6803 was achieved through heterologous expression of the fatty acyl-CoA/ACP reductase Maqu2220 from the bacteria Marinobacter aquaeolei VT8 and the fatty acyl-ACP reductase DPW from the rice Oryza sativa. These platform strains became models for testing multiplex CRISPR-interference (CRISPRi) metabolic engineering strategies to both improve fatty alcohol production and to study membrane homeostasis. CRISPRi allowed partial repression of up to six genes simultaneously, each encoding enzymes of acyl-ACP-consuming pathways...
November 30, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29196124/combined-engineering-of-disaccharide-transport-and-phosphorolysis-for-enhanced-atp-yield-from-sucrose-fermentation-in-saccharomyces-cerevisiae
#6
Wesley Leoricy Marques, Robert Mans, Ryan K Henderson, Eko Roy Marella, Jolanda Ter Horst, Erik de Hulster, Bert Poolman, Jean-Marc Daran, Jack T Pronk, Andreas K Gombert, Antonius J A van Maris
Anaerobic industrial fermentation processes do not require aeration and intensive mixing and the accompanying cost savings are beneficial for production of chemicals and fuels. However, the free-energy conservation of fermentative pathways is often insufficient for the production and export of the desired compounds and/or for cellular growth and maintenance. To increase free-energy conservation during fermentation of the industrially relevant disaccharide sucrose by Saccharomyces cerevisiae, we first replaced the native yeast α-glucosidases by an intracellular sucrose phosphorylase from Leuconostoc mesenteroides (LmSPase)...
November 28, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29196123/boosting-11-oxo-%C3%AE-amyrin-and-glycyrrhetinic-acid-synthesis-in-saccharomyces-cerevisiae-via-pairing-novel-oxidation-and-reduction-system-from-legume-plants
#7
Ming Zhu, Caixia Wang, Wentao Sun, Anqi Zhou, Ying Wang, Genlin Zhang, Xiaohong Zhou, Yixin Huo, Chun Li
Glycyrrhetinic acid (GA) and its precursor, 11-oxo-β-amyrin, are typical triterpenoids found in the roots of licorice, a traditional Chinese medicinal herb that exhibits diverse functions and physiological effects. In this study, we developed a novel and highly efficient pathway for the synthesis of GA and 11-oxo-β-amyrin in Saccharomyces cerevisiae by introducing efficient cytochrome P450s (CYP450s: Uni25647 and CYP72A63) and pairing their reduction systems from legume plants through transcriptome and genome-wide screening and identification...
November 28, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29191787/post-translational-regulation-of-metabolism-in-fumarate-hydratase-deficient-cancer-cells
#8
Emanuel Gonçalves, Marco Sciacovelli, Ana S H Costa, Maxine Gia Binh Tran, Timothy Isaac Johnson, Daniel Machado, Christian Frezza, Julio Saez-Rodriguez
Deregulated signal transduction and energy metabolism are hallmarks of cancer and both play a fundamental role in tumorigenesis. While it is increasingly recognised that signalling and metabolism are highly interconnected, the underpinning mechanisms of their co-regulation are still largely unknown. Here we designed and acquired proteomics, phosphoproteomics, and metabolomics experiments in fumarate hydratase (FH) deficient cells and developed a computational modelling approach to identify putative regulatory phosphorylation-sites of metabolic enzymes...
November 27, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29183749/heterologous-transporter-expression-for-improved-fatty-alcohol-secretion-in-yeast
#9
Yating Hu, Zhiwei Zhu, Jens Nielsen, Verena Siewers
The yeast Saccharomyces cerevisiae is an attractive host for industrial scale production of biofuels including fatty alcohols due to its robustness and tolerance towards harsh fermentation conditions. Many metabolic engineering strategies have been applied to generate high fatty alcohol production strains. However, impaired growth caused by fatty alcohol accumulation and high cost of extraction are factors limiting large-scale production. Here, we demonstrate that the use of heterologous transporters is a promising strategy to increase fatty alcohol production...
November 25, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29174524/engineering-cell-wall-synthesis-mechanism-for-enhanced-phb-accumulation-in-e-coli
#10
Xing-Chen Zhang, Yingying Guo, Xu Liu, Xin-Guang Chen, Qiong Wu, Guo-Qiang Chen
The rigidity of bacterial cell walls synthesized by a complicated pathway limit the cell shapes as coccus, bar or ellipse or even fibers. A less rigid bacterium could be beneficial for intracellular accumulation of poly-3-hydroxybutyrate (PHB) as granular inclusion bodies. To understand how cell rigidity affects PHB accumulation, E. coli cell wall synthesis pathway was reinforced and weakened, respectively. Cell rigidity was achieved by thickening the cell walls via insertion of a constitutive gltA (encoding citrate synthase) promoter in front of a series of cell wall synthesis genes on the chromosome of several E...
November 24, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29155059/microbial-production-of-branched-chain-dicarboxylate-2-methylsuccinic-acid-via-enoate-reductase-mediated-bioreduction
#11
Jian Wang, Yaping Yang, Ruihua Zhang, Xiaolin Shen, Zhenya Chen, Jia Wang, Qipeng Yuan, Yajun Yan
2-Methylsuccinic acid (2-MSA) is a C5 branched-chain dicarboxylate that serves as an attractive synthon for the synthesis of polymers with extensive applications in coatings, cosmetic solvents and bioplastics. However, the lack of natural pathways for 2-MSA biosynthesis has limited its application as a promising bio-replacement. Herein, we conceived a non-natural three-step biosynthetic route for 2-MSA, via employing the citramalate pathway in combination with enoate reductase-mediated bioreduction of the pathway intermediate citraconate...
November 20, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29155061/increasing-oxygen-availability-for-improving-poly-3-hydroxybutyrate-production-by-halomonas
#12
Pengfei Ouyang, Huan Wang, Ivan Hajnal, Qiong Wu, Yingying Guo, Guo-Qiang Chen
Technologies enabling high-cell-density growth are required for economical industrial production of most biotechnological products. However, the key factor limiting cell density in bioreactors is the availability of oxygen during the late phases of fermentation. Although the expression of bacterial Vitreoscilla hemoglobin (VHb) is useful for enhanced oxygen availability, bacterial cell membrane makes efficient hemoglobin-oxygen contact a challenge. On the other hand, periplasmic spaces of Gram-negative microorganisms offer an excellent compartment for the intermittent storage of hemoglobin-bound oxygen...
November 16, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29155060/controlling-cell-free-metabolism-through-physiochemical-perturbations
#13
Ashty S Karim, Jacob T Heggestad, Samantha A Crowe, Michael C Jewett
Building biosynthetic pathways and engineering metabolic reactions in cells can be time-consuming due to complexities in cellular metabolism. These complexities often convolute the combinatorial testing of biosynthetic pathway designs needed to define an optimal biosynthetic system. To simplify the optimization of biosynthetic systems, we recently reported a new cell-free framework for pathway construction and testing. In this framework, multiple crude-cell extracts are selectively enriched with individual pathway enzymes, which are then mixed to construct full biosynthetic pathways on the time scale of a day...
November 15, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29146470/combination-of-type-ii-fatty-acid-biosynthesis-enzymes-and-thiolases-supports-a-functional-%C3%AE-oxidation-reversal
#14
James M Clomburg, Stephanie C Contreras, Alexander Chou, Justin B Siegel, Ramon Gonzalez
An engineered reversal of the β-oxidation cycle (r-BOX) and the fatty acid biosynthesis (FAB) pathway are promising biological platforms for advanced fuel and chemical production in part due to their iterative nature supporting the synthesis of various chain length products. While diverging in their carbon-carbon elongation reaction mechanism, iterative operation of each pathway relies on common chemical conversions (reduction, dehydration, and reduction) differing only in the attached moiety (acyl carrier protein (ACP) in FAB vs Coenzyme A in r-BOX)...
November 13, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29129823/autonomous-control-of-metabolic-state-by-a-quorum-sensing-qs-mediated-regulator-for-bisabolene-production-in-engineered-e-coli
#15
Eun-Mi Kim, Han Min Woo, Tian Tian, Suzan Yilmaz, Pouya Javidpour, Jay D Keasling, Taek Soon Lee
Inducible gene expression systems are widely used in microbial host strains for protein and commodity chemical production because of their extensive characterization and ease of use. However, some of these systems have disadvantages such as leaky expression, lack of dynamic control, and the prohibitively high costs of inducers associated with large-scale production. Quorum sensing (QS) systems in bacteria control gene expression in response to population density, and the LuxI/R system from Vibrio fischeri is a well-studied example...
November 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29128647/a-mathematical-model-to-guide-genetic-engineering-of-photosynthetic-metabolism
#16
Giorgio Perin, Andrea Bernardi, Alessandra Bellan, Fabrizio Bezzo, Tomas Morosinotto
The optimization of algae biomass productivity in industrial cultivation systems requires genetic improvement of wild type strains isolated from nature. One of the main factors affecting algae productivity is their efficiency in converting light into chemical energy and this has been a major target of recent genetic efforts. However, photosynthetic productivity in algae cultures depends on many environmental parameters, making the identification of advantageous genotypes complex and the achievement of concrete improvements slow...
November 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29122703/improving-metabolic-efficiency-of-the-reverse-beta-oxidation-cycle-by-balancing-redox-cofactor-requirement
#17
Junjun Wu, Xia Zhang, Peng Zhou, Jiaying Huang, Xiudong Xia, Wei Li, Ziyu Zhou, Yue Chen, Yinghao Liu, Mingsheng Dong
Previous studies have made many exciting achievements on pushing the functional reversal of beta-oxidation cycle (r-BOX) to more widespread adoption for synthesis of a wide variety of fuels and chemicals. However, the redox cofactor requirement for the efficient operation of r-BOX remains unclear. In this work, the metabolic efficiency of r-BOX for medium-chain fatty acid (C6-C10, MCFA) production was optimized by redox cofactor engineering. Stoichiometric analysis of the r-BOX pathway and further experimental examination identified NADH as a crucial determinant of r-BOX process yield...
November 6, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29102594/a-systematically-chromosomally-engineered-escherichia-coli-efficiently-produces-butanol
#18
Hongjun Dong, Chunhua Zhao, Tianrui Zhang, Huawei Zhu, Zhao Lin, Wenwen Tao, Yanping Zhang, Yin Li
Biotechnological production of butanol in heterologous hosts has recently attracted many interests. Of the heterologous hosts investigated to date, engineered Escherichia coli has shown a superior butanol yield than the natural butanol-producing clostridial strains. However, all reported butanol-producing E. coli strains contain vectors and inducible promoters, which means antibiotics and inducers are required in the fermentation. The aim of this study was to develop a completely chromosomally engineered E...
November 2, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29101090/a-biosynthetic-route-for-polysialylating-proteins-in-escherichia-coli
#19
Timothy G Keys, Michael Wetter, Ivan Hang, Christoph Rutschmann, Simona Russo, Manuela Mally, Michael Steffen, Matthias Zuppiger, Fabian Müller, Jörg Schneider, Amirreza Faridmoayer, Chia-Wei Lin, Markus Aebi
Polysialic acid (polySia) is a posttranslational modification found on only a handful of proteins in the central nervous and immune systems. The addition of polySia to therapeutic proteins improves pharmacokinetics and reduces immunogenicity. To date, polysialylation of therapeutic proteins has only been achieved in vitro by chemical or chemoenzymatic strategies. In this work, we develop a biosynthetic pathway for site-specific polysialylation of recombinant proteins in the cytoplasm of Escherichia coli. The pathway takes advantage of a bacterial cytoplasmic polypeptide-glycosyltransferase to establish a site-specific primer on the target protein...
November 1, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29101089/comparison-of-the-metabolic-response-to-over-production-of-p-coumaric-acid-in-two-yeast-strains
#20
Angelica Rodriguez, Yun Chen, Sakda Khoomrung, Emre Özdemir, Irina Borodina, Jens Nielsen
The development of robust and efficient cell factories requires understanding of the metabolic changes triggered by the production of the targeted compound. Here we aimed to study how production of p-coumaric acid, a precursor of multiple secondary aromatic metabolites, influences the cellular metabolism of Saccharomyces cerevisiae. We evaluated the growth and p-coumaric acid production in batch and chemostat cultivations and analyzed the transcriptome and intracellular metabolome during steady state in low- and high-producers of p-coumaric acid in two strain backgrounds, S288c or CEN...
October 31, 2017: Metabolic Engineering
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