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Metabolic Engineering

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https://www.readbyqxmd.com/read/29775652/advances-and-prospects-of-bacillus-subtilis-cellular-factories-from-rational-design-to-industrial-applications
#1
REVIEW
Yang Gu, Xianhao Xu, Yaokang Wu, Tengfei Niu, Yanfeng Liu, Jianghua Li, Guocheng Du, Long Liu
Bacillus subtilis is the most characterized gram-positive bacterium that has significant attributes, such as growing well on cheap carbon sources, possessing clear inherited backgrounds, having mature genetic manipulation methods, and exhibiting robustness in large-scale fermentations. Till date, B. subtilis has been identified as attractive hosts for the production of recombinant proteins and chemicals. By applying various systems and synthetic biology tools, the productivity features of B. subtilis can be thoroughly analyzed and further optimized via metabolic engineering...
May 15, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29758287/pseudomonas-putida-as-a-functional-chassis-for-industrial-biocatalysis-from-native-biochemistry-to-trans-metabolism
#2
REVIEW
Pablo I Nikel, Víctor de Lorenzo
The itinerary followed by Pseudomonas putida from being a soil-dweller and plant colonizer bacterium to become a flexible and engineer-able platform for metabolic engineering stems from its natural lifestyle, which is adapted to harsh environmental conditions and all sorts of physicochemical stresses. Over the years, these properties have been capitalized biotechnologically owing to the expanding wealth of genetic tools designed for deep-editing the P. putida genome. A suite of dedicated vectors inspired in the core tenets of synthetic biology have enabled to suppress many of the naturally-occurring undesirable traits native to this species while enhancing its many appealing properties, and also to import catalytic activities and attributes from other biological systems...
May 11, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29753840/engineering-synergetic-co-2-fixing-pathways-for-malate-production
#3
Guipeng Hu, Jie Zhou, Xiulai Chen, Yuanyuan Qian, Cong Gao, Liang Guo, Peng Xu, Wei Chen, Jian Chen, Yin Li, Liming Liu
Increasing the microbial CO2 -fixing efficiency often requires supplying sufficient ATP and redirecting carbon flux for the production of metabolites. However, addressing these two issues concurrently remains a challenge. Here, we present a combinational strategy based on a synergetic CO2 -fixing pathway that combines an ATP-generating carboxylation reaction in the central metabolic pathway with the ATP-consuming RuBisCO shunt in the carbon fixation pathway. This strategy provides enough ATP to improve the efficiency of CO2 fixation and simultaneously rewires the CO2 -fixing pathway to the central metabolic pathway for the biosynthesis of chemicals...
May 10, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29753071/alterations-in-the-transcription-factors-gntr1-and-rama-enhance-the-growth-and-central-metabolism-of-corynebacterium-glutamicum
#4
Zhihao Wang, Jianming Liu, Lin Chen, An-Ping Zeng, Christian Solem, Peter Ruhdal Jensen
Evolution, i.e. the change in heritable characteristics of biological populations over successive generations, has created the diversity of life that exists today. In this study we have harnessed evolution to create faster growing mutants of Corynebacterium glutamicum, i.e. to debottleneck growth rate of this highly important industrial workhorse. After approximately 1500 generations of Adaptive Laboratory Evolution (ALE) in defined minimal medium with glucose, we obtained faster growing mutants with specific growth rate as high as 0...
May 9, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29753070/iterative-algorithm-guided-design-of-massive-strain-libraries-applied-to-itaconic-acid-production-in-yeast
#5
Eric M Young, Zheng Zhao, Bianca E M Gielesen, Liang Wu, D Benjamin Gordon, Johannes A Roubos, Christopher A Voigt
Metabolic engineering requires multiple rounds of strain construction to evaluate alternative pathways and enzyme concentrations. Optimizing multigene pathways stepwise or by randomly selecting enzymes and expression levels is inefficient. Here, we apply methods from design of experiments (DOE) to guide the construction of strain libraries from which the maximum information can be extracted without sampling every possible combination. We use Saccharomyces cerevisiae as a host for a novel six-gene pathway to itaconic acid, selected by comparing alternative shunt pathways that bypass the mitochondrial TCA cycle...
May 9, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29753069/engineering-a-short-aldolase-based-pathway-for-r-1-3-butanediol-production-in-escherichia-coli
#6
Kayla Nemr, Jonas E N Müller, Jeong Chan Joo, Pratish Gawand, Ruhi Choudhary, Burton Mendonca, Shuyi Lu, Xiuyan Yu, Alexander F Yakunin, Radhakrishnan Mahadevan
Microbial processes can produce a wide range of compounds; however, producing complex and long chain hydrocarbons remains a challenge. Aldol condensation offers a direct route to synthesize these challenging chemistries and can be catalyzed by microbes using aldolases. Deoxyribose-5-phosphate aldolase (DERA) condenses aldehydes and/or ketones to β-hydroxyaldehydes, which can be further converted to value-added chemicals such as a precursor to cholesterol-lowering drugs. Here, we implement a short, aldolase-based pathway in Escherichia coli to produce (R)-1,3-BDO from glucose, an essential component of pharmaceutical products and cosmetics...
May 9, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29751103/markerless-gene-knockout-and-integration-to-express-heterologous-biosynthetic-gene-clusters-in-pseudomonas-putida
#7
Kyeong Rok Choi, Jae Sung Cho, In Jin Cho, Dahyeon Park, Sang Yup Lee
Pseudomonas putida has gained much interest among metabolic engineers as a workhorse for producing valuable natural products. While a few gene knockout tools for P. putida have been reported, integration of heterologous genes into the chromosome of P. putida, an essential strategy to develop stable industrial strains producing heterologous bioproducts, requires development of a more efficient method. Current methods rely on time-consuming homologous recombination techniques and transposon-mediated random insertions...
May 8, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29733896/discovery-of-feed-forward-regulation-in-l-tryptophan-biosynthesis-and-its-use-in-metabolic-engineering-of-e-coli-for-efficient-tryptophan-bioproduction
#8
Lin Chen, Minliang Chen, Chengwei Ma, An-Ping Zeng
The L-tryptophan (Trp) biosynthesis pathway is highly regulated at multiple levels. The three types of regulations identified so far, namely repression, attenuation, and feedback inhibition have greatly impacted our understanding and engineering of cellular metabolism. In this study, feed-forward regulation is discovered as a novel regulation of this pathway and explored for engineering Escherichia coli for more efficient Trp biosynthesis. Specifically, indole glycerol phosphate synthase (IGPS) of the multifunctional enzyme TrpC from E...
May 4, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29729317/cellular-substrate-limitations-of-lysine-acetylation-turnover-by-sirtuins-investigated-with-engineered-futile-cycle-enzymes
#9
Svenja Heitmüller, Petra Neumann-Staubitz, Cornelia Herrfurth, Ivo Feussner, Heinz Neumann
Metabolic activity and epigenetic regulation of gene expression are intimately coupled. The mechanisms linking the two are incompletely understood. Sirtuins catalyse the removal of acetyl groups from lysine side chains of proteins using NAD+ as a stoichiometric cofactor, thereby connecting the acetylation state of histones to energy supply of the cell. Here, we investigate the impact of lysine acetylation turnover by sirtuins on cell physiology by engineering Sirtase, an enzyme that self-acetylates and deacetylates in futile cycles...
May 2, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29729316/optimal-bioprocess-design-through-a-gene-regulatory-network-growth-kinetic-hybrid-model-towards-replacing-monod-kinetics
#10
Argyro Tsipa, Michalis Koutinas, Chonlatep Usaku, Athanasios Mantalaris
Currently, design and optimisation of biotechnological bioprocesses is performed either through exhaustive experimentation and/or with the use of empirical, unstructured growth kinetics models. Whereas, elaborate systems biology approaches have been recently explored, mixed-substrate utilisation is predominantly ignored despite its significance in enhancing bioprocess performance. Herein, bioprocess optimisation for an industrially-relevant bioremediation process involving a mixture of highly toxic substrates, m-xylene and toluene, was achieved through application of a novel experimental-modelling gene regulatory network - growth kinetic (GRN-GK) hybrid framework...
May 2, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29715517/biosynthesis-of-d-glucaric-acid-from-sucrose-with-routed-carbon-distribution-in-metabolically-engineered-escherichia-coli
#11
Ya-Nan Qu, Hao-Jie Yan, Qiang Guo, Jia-Long Li, Yu-Cheng Ruan, Xiu-Zheng Yue, Wen-Xin Zheng, Tian-Wei Tan, Li-Hai Fan
D-glucaric acid is a promising platform compound used to synthesize many other value-added or commodity chemicals. The engineering of Escherichia coli for efficiently converting D-glucose to D-glucaric acid has been attempted for several years, with mixed sugar fermentation recently gaining growing interests due to the increased D-glucaric acid yield. Here, we co-expressed cscB, cscA, cscK, ino1, miox, udh, and suhB in E. coli BL21 (DE3), functionally constructing an unreported route from sucrose to D-glucaric acid...
April 30, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29719215/rewiring-fadr-regulon-for-the-selective-production-of-%C3%AF-hydroxy-palmitic-acid-from-glucose-in-escherichia-coli
#12
Joonwon Kim, Hee-Wang Yoo, Minsuk Kim, Eun-Jung Kim, Changmin Sung, Pyung-Gang Lee, Beom Gi Park, Byung-Gee Kim
ω-Hydroxy palmitic acid (ω-HPA) is a valuable compound for an ingredient of artificially synthesized ceramides and an additive for lubricants and adhesives. Production of such a fatty acid derivative is limited by chemical catalysis, but plausible by biocatalysis. However, its low productivity issue, including formations of unsaturated fatty acid (UFA) byproducts in host cells, remains as a hurdle toward industrial biological processes. In this study, to achieve selective and high-level production of ω-HPA from glucose in Escherichia coli, FadR, a native transcriptional regulator of fatty acid metabolism, and its regulon were engineered...
April 29, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29709649/lysine-production-from-the-sugar-alcohol-mannitol-design-of-the-cell-factory-corynebacterium-glutamicum-sea-3-through-integrated-analysis-and-engineering-of-metabolic-pathway-fluxes
#13
Sarah Lisa Hoffmann, Lukas Jungmann, Sarah Schiefelbein, Lindsay Peyriga, Edern Cahoreau, Jean-Charles Portais, Judith Becker, Christoph Wittmann
The amino acid lysine is among the world's most important biotechnological products, and enabling its manufacture from the most attractive new materials is an ever-present challenge. In this study, we describe a cell factory of Corynebacterium glutamicum, which produces lysine from mannitol. A preliminary mutant obtained by the deletion of the mannitol repressor MtlR in the glucose-based, lysine-producing C. glutamicum produced only small amounts of lysine. This limitation was due to the significant accumulation of fructose and a limited NADPH supply, which caused a low flux of only 6% into the oxidative pentose phosphate (PP) pathway...
April 27, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29704654/metabolic-engineering-of-pichia-pastoris
#14
REVIEW
David A Peña, Brigitte Gasser, Jürgen Zanghellini, Matthias G Steiger, Diethard Mattanovich
Besides its use for efficient production of recombinant proteins the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) has been increasingly employed as a platform to produce metabolites of varying origin. We summarize here the impressive methodological developments of the last years to model and analyze the metabolism of P. pastoris, and to engineer its genome and metabolic pathways. Efficient methods to insert, modify or delete genes via homologous recombination and CRISPR/Cas9, supported by modular cloning techniques, have been reported...
April 25, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29704653/exceeding-the-theoretical-fermentation-yield-in-mixotrophic-rubisco-based-engineered-escherichia-coli
#15
I-Ting Tseng, Yi-Ling Chen, Ching-Hsun Chen, Zhi-Xuan Shen, Cheng-Han Yang, Si-Yu Li
Rubisco-based engineered Escherichia coli MZLFB (E. coli BL21(DE3) Δzwf, Δldh, Δfrd) containing heterologous phosphoribulokinase (Prk) and Ribulose-1,5- bisphosphate carboxylase/oxygenase (Rubisco) was constructed for the mixotrophic growth. However, in situ CO2 recycling was hindered by clogs of pyruvate during glucose metabolism, which consequently resulted in an insufficient regeneration of NAD+ through the pflB-mediated ethanol production. Recombinant plasmid pLOI295 (encodes pyruvate decarboxylase and alcohol dehydrogenase II, referred to as the Pdc-based carbon tap valve (CTV) for convenience) was introduced into E...
April 25, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29702277/development-of-an-escherichia-coli-based-biocatalytic-system-for-the-efficient-synthesis-of-n-acetyl-d-neuraminic-acid
#16
Xianzhong Chen, Junbo Zhou, Lihua Zhang, Zhongji Pu, Liming Liu, Wei Shen, You Fan
N-acetyl-d-neuraminic acid (Neu5Ac) is a valuable resource that has seen increasing demand in both medicine and biotechnology. Although enzymatic systems and whole-cell biocatalysts have been developed for the synthesis of Neu5Ac, low yield and productivity still hamper the use of these methods on larger scales. We report the creation of an Escherichia coli biocatalyst for the efficient synthesis of Neu5Ac using a metabolic and protein engineering strategy. Expression of the two enzymes, N-acetyl-D-glucosamine 2-epimerase (AGE) and Neu5Ac lyase (NAL), was balanced using promoter engineering...
April 24, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29702276/rapidrip-quantifies-the-intracellular-metabolome-of-7-industrial-strains-of-e-coli
#17
Douglas McCloskey, Julia Xu, Lars Schrübbers, Hanne B Christensen, Markus J Herrgård
No abstract text is available yet for this article.
April 24, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29702275/recent-advances-in-metabolic-engineering-of-saccharomyces-cerevisiae-new-tools-and-their-applications
#18
REVIEW
Jiazhang Lian, Shekhar Mishra, Huimin Zhao
Metabolic engineering aims to develop efficient cell factories by rewiring cellular metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae has been extensively engineered to produce a wide variety of products at high levels from various feedstocks. In this review, we summarize the recent development of metabolic engineering approaches to modulate yeast metabolism with representative examples. Particularly, we highlight new tools for biosynthetic pathway optimization (i.e. combinatorial transcriptional engineering and dynamic metabolic flux control) and genome engineering (i...
April 24, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29702274/a-flow-cytometric-approach-to-engineering-escherichia-coli-for-improved-eukaryotic-protein-glycosylation
#19
Cameron J Glasscock, Laura E Yates, Thapakorn Jaroentomeechai, Joshua D Wilson, Judith H Merritt, Julius B Lucks, Mathew P DeLisa
A synthetic pathway for production of the eukaryotic trimannosyl chitobiose glycan (mannose3 -N-acetylglucosamine2 , Man3 GlcNAc2 ) and its transfer to specific asparagine residues in target proteins was previously engineered in Escherichia coli, providing this simple microbe with the ability to perform a complex post-translational protein modification. Here, we leveraged a flow cytometric fluorescence-based assay to improve Man3 GlcNAc2 glycan biosynthesis in E. coli cells. Specifically, pathway improvements were identified, including reducing pathway enzyme expression levels and overexpressing nucleotide sugar biosynthesis genes, which enhanced production of lipid-linked Man3 GlcNAc2 by nearly 50-fold to 13...
April 24, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29698778/a-comparative-analysis-of-single-cell-and-droplet-based-facs-for-improving-production-phenotypes-riboflavin-overproduction-in-yarrowia-lipolytica
#20
James M Wagner, Leqian Liu, Shuo-Fu Yuan, Maya V Venkataraman, Adam R Abate, Hal S Alper
Evolutionary approaches to strain engineering inherently require the identification of suitable selection techniques for the product and phenotype of interest. In this work, we undertake a comparative analysis of two related but functionally distinct methods of high-throughput screening: traditional single cell fluorescence activated cell sorting (single cell FACS) and microdroplet-enabled FACS (droplet FACS) using water/oil/water (w/o/w) emulsions. To do so, we first engineer and evolve the non-conventional yeast Yarrowia lipolytica for high extracellular production of riboflavin (vitamin B2), an innately fluorescent product...
April 23, 2018: Metabolic Engineering
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