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Metabolic engineering

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https://www.readbyqxmd.com/read/28805804/a-genetically-encoded-tool-for-manipulation-of-nadp-nadph-in-living-cells
#1
Valentin Cracan, Denis V Titov, Hongying Shen, Zenon Grabarek, Vamsi K Mootha
The redox coenzymes NADH and NADPH are broadly required for energy metabolism, biosynthesis and detoxification. Despite detailed knowledge of specific enzymes and pathways that utilize these coenzymes, a holistic understanding of the regulation and compartmentalization of NADH- and NADPH-dependent pathways is lacking, partly because of a lack of tools with which to investigate these processes in living cells. We have previously reported the use of the naturally occurring Lactobacillus brevis H2O-forming NADH oxidase (LbNOX) as a genetic tool for manipulation of the NAD(+)/NADH ratio in human cells...
August 7, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28805729/systems-biology-approach-to-bioremediation-of-nitroaromatics-constraint-based-analysis-of-2-4-6-trinitrotoluene-biotransformation-by-escherichia-coli
#2
Maryam Iman, Tabassom Sobati, Yunes Panahi, Meysam Mobasheri
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E...
August 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#3
Frank Delvigne, Ralf Takors, Rob Mudde, Walter van Gulik, Henk Noorman
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology...
August 14, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28804802/improvement-of-glycerol-catabolism-in-bacillus-licheniformis-for-production-of-poly-%C3%AE-glutamic-acid
#4
Yangyang Zhan, Chengjun Zhu, Bojie Sheng, Dongbo Cai, Qin Wang, Zhiyou Wen, Shouwen Chen
Bacillus licheniformis WX-02 is a well-studied strain to produce poly-γ-glutamic acid (γ-PGA) with numerous applications. This study is to improve WX-02 strain's capability of assimilating glycerol, a major byproduct of biofuels industries, through metabolic manipulation. Through gene knockout, the GlpK pathway was identified as the sole functional glycerol catabolism pathway, while the DhaK pathway was inactive for this strain under either aerobic or anaerobic conditions. The enhancement of glycerol utilization was attempted by substituting the native glpFK promoter with the constitutive promoter (P43), ytzE promoter (PytzE), and bacABC operon promoter (PbacA), respectively...
August 13, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28804512/engineering-shewanella-oneidensis-enables-xylose-fed-microbial-fuel-cell
#5
Feng Li, Yuanxiu Li, Liming Sun, Xiaofei Li, Changji Yin, Xingjuan An, Xiaoli Chen, Yao Tian, Hao Song
BACKGROUND: The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28803913/synthetic-rescue-couples-nadph-generation-to-metabolite-overproduction-in-saccharomyces-cerevisiae
#6
Siavash Partow, Patrick B Hyland, Radhakrishnan Mahadevan
Engineering the redox cofactor metabolism is known to be a key challenge in developing a platform strain for biosynthesis of valuable products. Hence, general strategies for manipulation of co-factor metabolism in industrially relevant hosts are of significance. Here, we demonstrate an improvement in α-ketoglutarate (AKG) production in S. cerevisiae using a novel approach based on synthetic rescue. Here, we first perturb the cytosolic NADPH metabolism via deletion of glucose-6-phosphate dehydrogenase (ZWF1)...
August 10, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28803776/mechanism-of-enzyme-repair-by-the-aaa-chaperone-rubisco-activase
#7
Javaid Y Bhat, Goran Miličić, Gabriel Thieulin-Pardo, Andreas Bracher, Andrew Maxwell, Susanne Ciniawsky, Oliver Mueller-Cajar, John R Engen, F Ulrich Hartl, Petra Wendler, Manajit Hayer-Hartl
How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco...
July 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28803364/volatile-terpenoids-multiple-functions-biosynthesis-modulation-and-manipulation-by-genetic-engineering
#8
REVIEW
Farhat Abbas, Yanguo Ke, Rangcai Yu, Yuechong Yue, Sikandar Amanullah, Muhammad Muzammil Jahangir, Yanping Fan
Terpenoids play several physiological and ecological functions in plant life through direct and indirect plant defenses and also in human society because of their enormous applications in the pharmaceutical, food and cosmetics industries. Through the aid of genetic engineering its role can by magnified to broad spectrum by improving genetic ability of crop plants, enhancing the aroma quality of fruits and flowers and the production of pharmaceutical terpenoids contents in medicinal plants. Terpenoids are structurally diverse and the most abundant plant secondary metabolites, playing an important role in plant life through direct and indirect plant defenses, by attracting pollinators and through different interactions between the plants and their environment...
August 12, 2017: Planta
https://www.readbyqxmd.com/read/28802003/recombinant-lactococcus-lactis-for-efficient-conversion-of-cellodextrins-into-l-lactic-acid
#9
Chiara Gandini, Loredana Tarraran, Denis Kalemasi, Enrica Pessione, Roberto Mazzoli
Lactic acid bacteria (LAB) are among the most interesting organisms for industrial processes with a long history of application as food starters and biocontrol agents, and an underexploited potential for biorefineries converting biomass into high-value compounds. Lactic acid (LA), their main fermentation product, is among the most requested chemicals owing to its broad range of applications. Notably, LA polymers, i.e., polylactides, have high potential as biodegradable substitutes of fossil-derived plastics...
August 12, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28801604/recombineering-using-recet-in-corynebacterium-glutamicum-atcc14067-via-a-self-excisable-cassette
#10
Yuanyuan Huang, Lu Li, Shan Xie, Nannan Zhao, Shuangyan Han, Ying Lin, Suiping Zheng
Gene manipulation is essential for metabolic engineering and synthetic biology, but the current general gene manipulation methods are not applicable to the non-model strain Corynebacterium glutamicum (C. glutamicum) ATCC14067, which is used for amino acid production. Here, we report an effective and sequential deletion method for C. glutamicum ATCC14067 using the exonuclease-recombinase pair RecE + RecT (RecET) for recombineering via a designed self-excisable linear double-strand DNA (dsDNA) cassette, which contains the Cre/loxP system, to accomplish markerless deletion...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801067/dna-methylation-in-cho-cells
#11
Anna Wippermann, Thomas Noll
Chinese hamster ovary (CHO) cells account for the production of the majority of biopharmaceutical molecules - however, the molecular basis for their versatile properties is not entirely understood yet and the underlying cellular processes need to be characterized in detail. One such process that is supposed to contribute significantly to CHO cell phenotype is methylation of DNA at cytosine residues. DNA methylation was shown to be involved in several central biological processes in humans and to contribute to diseases like cancer...
August 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28800966/reconstruction-of-a-metabolic-regulatory-network-in-escherichia-coli-for-purposeful-switching-from-cell-growth-mode-to-production-mode-in-direct-gaba-fermentation-from-glucose
#12
Yuki Soma, Yuri Fujiwara, Takuya Nakagawa, Keigo Tsuruno, Taizo Hanai
γ-aminobutyric acid (GABA) is a drug and functional food additive and is used as a monomer for producing the biodegradable plastic, polyamide 4. Recently, direct GABA fermentation from glucose has been developed as an alternative to glutamate-based whole cell bioconversion. Although total productivity in fermentation is determined by the specific productivity and cell amount responsible for GABA production, the optimal metabolic state for GABA production conflicts with that for bacterial cell growth. Herein, we demonstrated metabolic state switching from the cell growth mode based on the metabolic pathways of the wild type strain to a GABA production mode based on a synthetic metabolic pathway in Escherichia coli through rewriting of the metabolic regulatory network and pathway engineering...
August 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28800965/the-crispr-cas9-facilitated-multiplex-pathway-optimization-cfpo-technique-and-its-application-to-improve-the-escherichia-coli-xylose-utilization-pathway
#13
Xinna Zhu, Dongdong Zhao, Huanna Qiu, Feiyu Fan, Shuli Man, Changhao Bi, Xueli Zhang
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome...
August 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28799209/computation-guided-design-of-a-stimulus-responsive-multi-enzyme-supramolecular-assembly
#14
Lu Yang, Elliott M Dolan, Sophia K Tan, Tianyun Lin, Eduardo D Sontag, Sagar Khare
The construction of stimulus-responsive supramolecular complexes of metabolic pathway enzymes, inspired by natural multi-enzyme assemblies (metabolons), provides an attractive avenue for efficient and spatio-temporally controllable one-pot biotransformations. We constructed a phosphorylation- and optically-responsive metabolon for the biodegradation of the environmental pollutant 1,2,3-trichloropropane (TCP). The three enzymes in of a synthetic degradation pathway were fused to engineered variants of the peptide-binding domains (SH2, SH3; the latter redesigned to incorporate an unnatural photocrosslinkable amino acid) or their corresponding binding peptides, and enzyme co-localization in response to phosphorylation and UV-light was demonstrated...
August 10, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28796489/rational-modular-rna-engineering-based-on-in-vivo-profiling-of-structural-accessibility
#15
Abigail N Leistra, Paul Amador, Aishwarya Buvanendiran, Alex Moon-Walker, Lydia M Contreras
Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28796289/medicine-is-not-health-care-food-is-health-care-plant-metabolic-engineering-diet-and-human-health
#16
REVIEW
Cathie Martin, Jie Li
Contents I. II. III. IV. V. VI. References SUMMARY: Plants make substantial contributions to our health through our diets, providing macronutrients for energy and growth as well as essential vitamins and phytonutrients that protect us from chronic diseases. Imbalances in our food can lead to deficiency diseases or obesity and associated metabolic disorders, increased risk of cardiovascular diseases and cancer. Nutritional security is now a global challenge which can be addressed, at least in part, through plant metabolic engineering for nutritional improvement of foods that are accessible to and eaten by many...
August 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28795570/rapid-and-scalable-preparation-of-bacterial-lysates-for-cell-free-gene-expression
#17
Andriy Didovyk, Taishi Tonooka, Lev Tsimring, Jeff Hasty
Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducible, and a labor- and cost-effective approach for rapid production of bacterial lysates for cell-free gene expression. Using this method, robust and highly active bacterial cell lysates can be produced without specialized equipment at a wide range of scales, making cell-free gene expression easily and broadly accessible...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28793788/improvements-in-algal-lipid-production-a-systems-biology-and-gene-editing-approach
#18
Avik Banerjee, Chiranjib Banerjee, Sangeeta Negi, Jo-Shu Chang, Pratyoosh Shukla
BACKGROUND: In the wake of rising energy demands, microalgae have emerged as potential sources of sustainable and renewable carbon-neutral fuels, such as bio-hydrogen and bio-oil. PURPOSE: For rational metabolic engineering, the elucidation of metabolic pathways in fine detail and their manipulation according to requirements is the key to exploiting the use of microalgae. Emergence of site-specific nucleases have revolutionized applied research leading to biotechnological gains...
August 9, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28792758/profiling-of-microbial-colonies-for-high-throughput-engineering-of-multi-step-enzymatic-reactions-via-optically-guided-maldi-ms
#19
Tong Si, Bin Li, Troy J Comi, Yuwei Wu, Pingfan Hu, Yuying Wu, Yuhao Min, Douglas A Mitchell, Huimin Zhao, Jonathan V Sweedler
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-free method for high-throughput engineering of multi-step biochemical reactions based on optically guided MALDI-ToF MS analysis of bacterial colonies. The bacterial cells provide containment of multiple enzymes and access to substrates and cofactors via metabolism. Automated MALDI-ToF MS acquisition from randomly distributed colonies simplifies procedures to prepare strain libraries without liquid handling...
August 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28792090/distinct-activation-mechanisms-trigger-the-trypanocidal-activity-of-dna-damaging-prodrugs
#20
Emma Louise Meredith, Ambika Kumar, Aya Konno, Joanna Szular, Sam Alsford, Karin Seifert, David Horn, Shane R Wilkinson
Quinone-based compounds have been exploited to treat infectious diseases and cancer, with such chemicals often functioning as inhibitors of key metabolic pathways or as prodrugs. Here, we screened an aziridinyl-1,4-benzoquinone (ABQ) library against the causative agents of trypanosomiasis, and cutaneous leishmaniasis, identifying several potent structures that exhibited EC50 values of <100 nM. However, these compounds also displayed significant toxicity towards mammalian cells indicating that they are not suitable therapies for systemic infections...
August 9, 2017: Molecular Microbiology
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