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Metabolic Engineering Communications

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https://www.readbyqxmd.com/read/30009131/engineering-redox-balanced-ethanol-production-in-the-cellulolytic-and-extremely-thermophilic-bacterium-caldicellulosiruptor-bescii
#1
Amanda M Williams-Rhaesa, Gabriel M Rubinstein, Israel M Scott, Gina L Lipscomb, Farris L Poole Ii, Robert M Kelly, Michael W W Adams
Caldicellulosiruptor bescii is an extremely thermophilic cellulolytic bacterium with great potential for consolidated bioprocessing of renewable plant biomass. Since it does not natively produce ethanol, metabolic engineering is required to create strains with this capability. Previous efforts involved the heterologous expression of the gene encoding a bifunctional alcohol dehydrogenase, AdhE, which uses NADH as the electron donor to reduce acetyl-CoA to ethanol. Acetyl-CoA produced from sugar oxidation also generates reduced ferredoxin but there is no known pathway for the transfer of electrons from reduced ferredoxin to NAD in C...
December 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29896448/identification-of-parallel-and-divergent-optimization-solutions-for-homologous-metabolic-enzymes
#2
Robert F Standaert, Richard J Giannone, Joshua K Michener
Metabolic pathway assembly typically involves the expression of enzymes from multiple organisms in a single heterologous host. Ensuring that each enzyme functions effectively can be challenging, since many potential factors can disrupt proper pathway flux. Here, we compared the performance of two enzyme homologs in a pathway engineered to allow Escherichia coli to grow on 4-hydroxybenzoate (4-HB), a byproduct of lignocellulosic biomass deconstruction. Single chromosomal copies of the 4-HB 3-monooxygenase genes pobA and praI , from Pseudomonas putida KT2440 and Paenibacillus sp...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29896447/a-novel-chimaeric-flocculation-protein-enhances-flocculation-in-saccharomyces-cerevisiae
#3
Johan O Westman, Jonas Nyman, Richard M A Manara, Valeria Mapelli, Carl Johan Franzén
Yeast flocculation is the reversible formation of multicellular complexes mediated by lectin-like cell wall proteins binding to neighbouring cells. Strong flocculation can improve the inhibitor tolerance and fermentation performance of yeast cells in second generation bioethanol production. The strength of flocculation increases with the size of the flocculation protein and is strain dependent. However, the large number of internal repeats in the sequence of FLO1 from Saccharomyces cerevisiae S288c makes it difficult to recombinantly express the gene to its full length...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29896446/alleviation-of-reactive-oxygen-species-enhances-pufa-accumulation-in-schizochytrium-sp-through-regulating-genes-involved-in-lipid-metabolism
#4
Sai Zhang, Yaodong He, Biswarup Sen, Xiaohong Chen, Yunxuan Xie, Jay D Keasling, Guangyi Wang
The unicellular heterotrophic thraustochytrids are attractive candidates for commercial polyunsaturated fatty acids (PUFA) production. However, the reactive oxygen species (ROS) generated in their aerobic fermentation process often limits their PUFA titer. Yet, the specific mechanisms of ROS involvement in the crosstalk between oxidative stress and intracellular lipid synthesis remain poorly described. Metabolic engineering to improve the PUFA yield in thraustochytrids without compromising growth is an important aspect of economic feasibility...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29896445/metabolic-engineering-of-saccharomyces-cerevisiae-for-overproduction-of-triacylglycerols
#5
Raphael Ferreira, Paulo Gonçalves Teixeira, Michael Gossing, Florian David, Verena Siewers, Jens Nielsen
Triacylglycerols (TAGs) are valuable versatile compounds that can be used as metabolites for nutrition and health, as well as feedstocks for biofuel production. Although Saccharomyces cerevisiae is the favored microbial cell factory for industrial production of biochemicals, it does not produce large amounts of lipids and TAGs comprise only ~1% of its cell dry weight. Here, we engineered S. cerevisiae to reorient its metabolism for overproduction of TAGs, by regulating lipid droplet associated-proteins involved in TAG synthesis and hydrolysis...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29765865/a-protocatechuate-biosensor-for-pseudomonas-putida-kt2440-via-promoter-and-protein-evolution
#6
Ramesh K Jha, Jeremy M Bingen, Christopher W Johnson, Theresa L Kern, Payal Khanna, Daniel S Trettel, Charlie E M Strauss, Gregg T Beckham, Taraka Dale
Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29487800/biocatalytic-production-of-adipic-acid-from-glucose-using-engineered-saccharomyces-cerevisiae
#7
Kaushik Raj, Siavash Partow, Kevin Correia, Anna N Khusnutdinova, Alexander F Yakunin, Radhakrishnan Mahadevan
Adipic acid is an important industrial chemical used in the synthesis of nylon-6,6. The commercial synthesis of adipic acid uses petroleum-derived benzene and releases significant quantities of greenhouse gases. Biocatalytic production of adipic acid from renewable feedstocks could potentially reduce the environmental damage and eliminate the need for fossil fuel precursors. Recently, we have demonstrated the first enzymatic hydrogenation of muconic acid to adipic acid using microbial enoate reductases (ERs) - complex iron-sulfur and flavin containing enzymes...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29349039/engineering-escherichia-coli-for-the-production-of-terpene-mixture-enriched-in-caryophyllene-and-caryophyllene-alcohol-as-potential-aviation-fuel-compounds
#8
Weihua Wu, Fang Liu, Ryan W Davis
Recent studies have revealed that caryophyllene and its stereoisomers not only exhibit multiple biological activities but also have desired properties as renewable candidates for ground transportation and jet fuel applications. This study presents the first significant production of caryophyllene and caryolan-1-ol by an engineered E. coli with heterologous expression of mevalonate pathway genes with a caryophyllene synthase and a caryolan-1-ol synthase. By optimizing metabolic flux and fermentation parameters, the engineered strains yielded 449 mg/L of total terpene, including 406 mg/L sesquiterpene with 100 mg/L caryophyllene and 10 mg/L caryolan-1-ol...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29255672/genome-scale-model-guided-design-of-propionibacterium-for-enhanced-propionic-acid-production
#9
Laura Navone, Tim McCubbin, Ricardo A Gonzalez-Garcia, Lars K Nielsen, Esteban Marcellin
Production of propionic acid by fermentation of propionibacteria has gained increasing attention in the past few years. However, biomanufacturing of propionic acid cannot compete with the current oxo-petrochemical synthesis process due to its well-established infrastructure, low oil prices and the high downstream purification costs of microbial production. Strain improvement to increase propionic acid yield is the best alternative to reduce downstream purification costs. The recent generation of genome-scale models for a number of Propionibacterium species facilitates the rational design of metabolic engineering strategies and provides a new opportunity to explore the metabolic potential of the Wood-Werkman cycle...
June 2018: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188187/genome-sequence-and-analysis-of-escherichia-coli-production-strain-ls5218
#10
Jacqueline M Rand, Gina C Gordon, Christopher R Mehrer, Brian F Pfleger
Escherichia coli strain LS5218 is a useful host for the production of fatty acid derived products, but the genetics underlying this utility have not been fully investigated. Here, we report the genome sequence of LS5218 and a list of large mutations and single nucleotide permutations (SNPs) relative to E. coli K-12 strain MG1655. We discuss how genetic differences may affect the physiological differences between LS5218 and MG1655. We find that LS5218 is more closely related to E. coli strain NCM3722 and suspect that small genetic differences between K-12 derived strains may have a significant impact on metabolic engineering efforts...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188186/yalibricks-a-versatile-genetic-toolkit-for-streamlined-and-rapid-pathway-engineering-in-yarrowia-lipolytica
#11
Lynn Wong, Jake Engel, Erqing Jin, Benjamin Holdridge, Peng Xu
Effective metabolic engineering of microorganisms relies on balanced expression of both heterologous and endogenous genes to channel metabolic flux towards products of interest while achieving reasonable biomass buildup. To facilitate combinatorial pathway engineering and facile genetic operation, we engineered a set of modular cloning vectors compatible with BioBrick standards, called YaliBricks, to allow for rapid assembly of multigene pathways with customized genetic control elements (promoters, intronic sequences and terminators) in the oleaginous yeast Yarrowia lipolytica ...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188185/metabolic-engineering-of-schizosaccharomyces-pombe-via-crispr-cas9-genome-editing-for-lactic-acid-production-from-glucose-and-cellobiose
#12
Aiko Ozaki, Rie Konishi, Chisako Otomo, Mayumi Kishida, Seiya Takayama, Takuya Matsumoto, Tsutomu Tanaka, Akihiko Kondo
Modification of the Schizosaccharomyces pombe genome is often laborious, time consuming due to the lower efficiency of homologous recombination. Here, we constructed metabolically engineered S. pombe strains using a CRISPR-Cas9 system and also demonstrated D-lactic acid (D-LA) production from glucose and cellobiose. Genes encoding two separate pyruvate decarboxylases (PDCs), an L-lactic acid dehydrogenase (L-LDH), and a minor alcohol dehydrogenase (SPBC337.11) were disrupted, thereby attenuating ethanol production...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188184/up-finder-a-cobra-toolbox-extension-for-identifying-gene-overexpression-strategies-for-targeted-overproduction
#13
Xi Wang, Liang Yu, Shulin Chen
Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox under MATLAB environment. All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188183/isobutanol-production-in-synechocystis-pcc-6803-using-heterologous-and-endogenous-alcohol-dehydrogenases
#14
Rui Miao, Xufeng Liu, Elias Englund, Pia Lindberg, Peter Lindblad
Isobutanol is a flammable compound that can be used as a biofuel due to its high energy density and suitable physical and chemical properties. In this study, we examined the capacity of engineered strains of Synechocystis PCC 6803 containing the α-ketoisovalerate decarboxylase from Lactococcus lactis and different heterologous and endogenous alcohol dehydrogenases (ADH) for isobutanol production. A strain expressing an introduced kivd without any additional copy of ADH produced 3 mg L-1 OD750 -1 isobutanol in 6 days...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188182/a-comprehensive-evaluation-of-constraining-amino-acid-biosynthesis-in-compartmented-models-for-metabolic-flux-analysis
#15
Mathias Lehnen, Birgitta E Ebert, Lars M Blank
Recent advances in the availability and applicability of genetic tools for non-conventional yeasts have raised high hopes regarding the industrial applications of such yeasts; however, quantitative physiological data on these yeasts, including intracellular flux distributions, are scarce and have rarely aided in the development of novel yeast applications. The compartmentation of eukaryotic cells adds to model complexity. Model constraints are ideally based on biochemical evidence, which is rarely available for non-conventional yeast and eukaryotic cells...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188181/eliminating-a-global-regulator-of-carbon-catabolite-repression-enhances-the-conversion-of-aromatic-lignin-monomers-to-muconate-in-pseudomonas-putida-kt2440
#16
Christopher W Johnson, Paul E Abraham, Jeffrey G Linger, Payal Khanna, Robert L Hettich, Gregg T Beckham
Carbon catabolite repression refers to the preference of microbes to metabolize certain growth substrates over others in response to a variety of regulatory mechanisms. Such preferences are important for the fitness of organisms in their natural environments, but may hinder their performance as domesticated microbial cell factories. In a Pseudomonas putida KT2440 strain engineered to convert lignin-derived aromatic monomers such as p -coumarate and ferulate to muconate, a precursor to bio-based nylon and other chemicals, metabolic intermediates including 4-hydroxybenzoate and vanillate accumulate and subsequently reduce productivity...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188180/comparison-of-orthologous-cyanobacterial-aldehyde-deformylating-oxygenases-in-the-production-of-volatile-c3-c7-alkanes-in-engineered-e-coli
#17
Pekka Patrikainen, Veronica Carbonell, Kati Thiel, Eva-Mari Aro, Pauli Kallio
Aldehyde deformylating oxygenase (ADO) is a unique enzyme found exclusively in photosynthetic cyanobacteria, which natively converts acyl aldehyde precursors into hydrocarbon products embedded in cellular lipid bilayers. This capacity has opened doors for potential biotechnological applications aiming at biological production of diesel-range alkanes and alkenes, which are compatible with the nonrenewable petroleum-derived end-products in current use. The development of production platforms, however, has been limited by the relative inefficiency of ADO enzyme, promoting research towards finding new strategies and information to be used for rational design of enhanced pathways for hydrocarbon over-expression...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29188179/development-of-a-high-efficiency-integration-system-and-promoter-library-for-rapid-modification-of-pseudomonas-putida-kt2440
#18
Joshua R Elmore, Anna Furches, Gara N Wolff, Kent Gorday, Adam M Guss
Pseudomonas putida strains are highly robust bacteria known for their ability to efficiently utilize a variety of carbon sources, including aliphatic and aromatic hydrocarbons. Recently, P. putida has been engineered to valorize the lignin stream of a lignocellulosic biomass pretreatment process. Nonetheless, when compared to platform organisms such as Escherichia coli , the toolkit for engineering P. putida is underdeveloped. Heterologous gene expression in particular is problematic. Plasmid instability and copy number variance provide challenges for replicative plasmids, while use of homologous recombination for insertion of DNA into the chromosome is slow and laborious...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/28989864/flux-balance-analysis-indicates-that-methane-is-the-lowest-cost-feedstock-for-microbial-cell-factories
#19
Austin D Comer, Matthew R Long, Jennifer L Reed, Brian F Pfleger
The low cost of natural gas has driven significant interest in using C1 carbon sources (e.g. methane, methanol, CO, syngas) as feedstocks for producing liquid transportation fuels and commodity chemicals. Given the large contribution of sugar and lignocellulosic feedstocks to biorefinery operating costs, natural gas and other C1 sources may provide an economic advantage. To assess the relative costs of these feedstocks, we performed flux balance analysis on genome-scale metabolic models to calculate the maximum theoretical yields of chemical products from methane, methanol, acetate, and glucose...
December 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29468131/selection-finder-selfi-a-computational-metabolic-engineering-tool-to-enable-directed-evolution-of-enzymes
#20
Neda Hassanpour, Ehsan Ullah, Mona Yousofshahi, Nikhil U Nair, Soha Hassoun
Directed evolution of enzymes consists of an iterative process of creating mutant libraries and choosing desired phenotypes through screening or selection until the enzymatic activity reaches a desired goal. The biggest challenge in directed enzyme evolution is identifying high-throughput screens or selections to isolate the variant(s) with the desired property. We present in this paper a computational metabolic engineering framework, Selection Finder (SelFi), to construct a selection pathway from a desired enzymatic product to a cellular host and to couple the pathway with cell survival...
June 2017: Metabolic Engineering Communications
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