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Metabolic engineering

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https://www.readbyqxmd.com/read/29785207/promiscuous-activities-of-heterologous-enzymes-lead-to-unintended-metabolic-rerouting-in-saccharomyces-cerevisiae-engineered-to-assimilate-various-sugars-from-renewable-biomass
#1
Eun Ju Yun, Eun Joong Oh, Jing-Jing Liu, Sora Yu, Dong Hyun Kim, Suryang Kwak, Kyoung Heon Kim, Yong-Su Jin
Background: Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae . Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29783732/hyaluronic-acid-influence-on-normal-and-osteoarthritic-tissue-engineered-cartilage
#2
Shabnam Hemmati-Sadeghi, Jochen Ringe, Tilo Dehne, Rainer Haag, Michael Sittinger
The aim of this study is to identify gene expression profiles associated with hyaluronic acid (HA) treatment of normal and osteoarthritis (OA)-like tissue-engineered cartilage. 3D cartilage micromasses were treated with tumour necrosis factor-α (TNF-α) (OA-inducer) and/or HA for 7 days. Viability was examined by PI/FDA staining. To document extracellular matrix (ECM) formation, glycosaminoglycans (GAG) were stained with Safranin-O and cartilage-specific type II collagen was detected immunohistochemically...
May 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29782142/projection-based-3d-printing-of-cell-patterning-scaffolds-with-multi-scale-channels
#3
Dai Xue, Yancheng Wang, Jiaxin Zhang, Deqing Mei, Yue Wang, Shaochen Chen
To fully actualize artificial, cell-laden biological models in tissue engineering, such as 3D organoids and organs-on-a-chip systems, cells need to be patterned such that they can precisely mimic natural microenvironments in vitro. Despite increasing interest in this area, patterning cells at multiscales (~10 μm - 10 mm) remains a significant challenge in bioengineering. Here we report a projection-based 3D printing system that achieves rapid and high-resolution fabrication of hydrogel scaffolds featuring intricate channels for multi-scale cell patterning...
May 21, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29780558/long-lived-protein-expression-in-hydrogel-particles-towards-artificial-cells
#4
Xiaoyu Zhou, Han Wu, Miao Cui, Sze Nga Lai, Bo Zheng
Herein we report a new type of cell-mimic particle capable of long-lived protein expression. We constructed the cell-mimic particles by immobilizing the proteinaceous factors of the cell-free transcription and translation system on the polymer backbone of hydrogel particles and encapsulating the plasmid template and ribosome inside the hydrogel. With the continuous supply of nutrients and energy, the protein expression in the cell-mimic particles remained stable for at least 11 days. We achieved the regulation of protein expression in the cell-mimic particles by the usage of lac operon...
May 14, 2018: Chemical Science
https://www.readbyqxmd.com/read/29779127/physiological-and-transcriptomic-analysis-of-a-chronologically-long-lived-saccharomyces-cerevisiae-strain-obtained-by-evolutionary-engineering
#5
Mevlüt Arslan, Can Holyavkin, Halil İbrahim Kısakesen, Alican Topaloğlu, Yusuf Sürmeli, Zeynep Petek Çakar
High-throughput aging studies with yeast as a model organism involve transposon-mutagenesis and yeast knockout collection, which have been pivotal strategies for understanding the complex cellular aging process. In this study, a chronologically long-lived Saccharomyces cerevisiae mutant was successfully obtained by using another high-throughput approach, evolutionary engineering, based on systematic selection in successive batch cultures under gradually increasing levels of caloric restriction. Detailed comparative physiological and transcriptomic analyses of the chronologically long-lived mutant and the reference strain revealed enhanced levels of respiratory metabolism, upregulation of genes related to carbohydrate metabolic processes, glycogen-trehalose pathways, stress response, and repression of protein synthesis-related genes in the long-lived mutant SRM11, already in the absence of caloric restriction...
May 19, 2018: Molecular Biotechnology
https://www.readbyqxmd.com/read/29778216/nitric-oxide-signalling-in-yeast
#6
Rika I Astuti, Ryo Nasuno, Hiroshi Takagi
Nitric oxide (NO) is a cellular signalling molecule widely conserved among organisms, including microorganisms such as bacteria, yeasts, and fungi, and higher eukaryotes such as plants and mammals. NO is mainly produced by the activities of NO synthase (NOS) or nitrite reductase (NIR). There are several NO detoxification systems, including NO dioxygenase (NOD) and S-nitrosoglutathione reductase (GSNOR). NO homeostasis, based on the balance between NO synthesis and degradation, is important for regulating its physiological functions, since an excess of NO causes nitrosative stress due to the high reactivity of NO and NO-derived compounds...
2018: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/29777596/morphological-analysis-of-pore-size-and-connectivity-in-a-thick-mixed-culture-biofilm
#7
Alex F Rosenthal, James S Griffin, Michael Wagner, Aaron I Packman, Oluwaseyi Balogun, George F Wells
Morphological parameters are commonly used to predict transport and metabolic kinetics in biofilms. Yet, quantification of biofilm morphology remains challenging due to imaging technology limitations and lack of robust analytical approaches. We present a novel set of imaging and image analysis techniques to estimate internal porosity, pore size distributions, and pore network connectivity to a depth of 1 mm at a resolution of 10 µm in a biofilm exhibiting both heterotrophic and nitrifying activity. Optical coherence tomography (OCT) scans revealed an extensive pore network with diameters as large as 110 µm directly connected to the biofilm surface and surrounding fluid...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777103/bacterial-encapsulins-as-orthogonal-compartments-for-mammalian-cell-engineering
#8
Felix Sigmund, Christoph Massner, Philipp Erdmann, Anja Stelzl, Hannes Rolbieski, Mitul Desai, Sarah Bricault, Tobias P Wörner, Joost Snijder, Arie Geerlof, Helmut Fuchs, Martin Hrabĕ de Angelis, Albert J R Heck, Alan Jasanoff, Vasilis Ntziachristos, Jürgen Plitzko, Gil G Westmeyer
We genetically controlled compartmentalization in eukaryotic cells by heterologous expression of bacterial encapsulin shell and cargo proteins to engineer enclosed enzymatic reactions and size-constrained metal biomineralization. The shell protein (EncA) from Myxococcus xanthus auto-assembles into nanocompartments inside mammalian cells to which sets of native (EncB,C,D) and engineered cargo proteins self-target enabling localized bimolecular fluorescence and enzyme complementation. Encapsulation of the enzyme tyrosinase leads to the confinement of toxic melanin production for robust detection via multispectral optoacoustic tomography (MSOT)...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29776927/ecological-engineering-helps-maximize-function-in-algal-oil-production
#9
Sara L Jackrel, Anita Narwani, Bastian Bentlage, Robert B Levine, David C Hietala, Phillip E Savage, Todd H Oakley, Vincent J Denef, Bradley J Cardinale
Algal biofuels have the potential to curb emissions of greenhouse gases from fossil fuels, but current growing methods fail to produce fuels that meet the multiple standards necessary for economical industrial use. For example, algae grown as monocultures for biofuel production have not simultaneously and economically achieved high yields of the high-quality, lipid-rich biomass desired for the industrial-scale production of bio-oil. Decades of study in the field of ecology have demonstrated that simultaneous increases in multiple functions, such as the quantity and quality of biomass, can occur in natural ecosystems by increasing biological diversity...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29775852/biomimetic-magnetoelectric-nanocrystals-synthesized-by-polymerization-of-heme-as-advanced-nanomaterials-for-biosensing-application
#10
Jeong Eun Hyeon, Da Woon Jeong, Young Jin Ko, Seung Wook Kim, Chulhwan Park, Sung Ok Han
Regardless of the malaria disease risk, the malaria parasite Plasmodium falciparum has an interesting mechanism. During its growth within the red blood cell, toxic free heme is converted into an insoluble crystalline form called the malaria pigment, or hemozoin. In particular, natural hemozoin nanocrystals can provide multiple applications in biosensing fields for health care and diagnosis as similar to artificial metal nanoparticles. In this study, the heme was biologically synthesized and polymerized by Corynebacterium glutamicum and final polymer was applied as a biomimetic conductive biopolymer...
May 10, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29775652/advances-and-prospects-of-bacillus-subtilis-cellular-factories-from-rational-design-to-industrial-applications
#11
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/29774011/metabolomics-analysis-of-the-toxic-effects-of-the-production-of-lycopene-and-its-precursors
#12
April M Miguez, Monica P McNerney, Mark P Styczynski
Using cells as microbial factories enables highly specific production of chemicals with many advantages over chemical syntheses. A number of exciting new applications of this approach are in the area of precision metabolic engineering, which focuses on improving the specificity of target production. In recent work, we have used precision metabolic engineering to design lycopene-producing Escherichia coli for use as a low-cost diagnostic biosensor. To increase precursor availability and thus the rate of lycopene production, we heterologously expressed the mevalonate pathway...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773508/comparative-proteomic-analyses-of-hyphozyma-roseonigra-atcc-20624-in-response-to-sclareol
#13
Xiuwen Wang, Xiaohua Zhang, Qingshou Yao, Dongliang Hua, Jiayang Qin
Sclareol is an important intermediate for ambroxide synthesis industries. Hyphozyma roseonigra ATCC 20624 was the only reported strain capable of degrading sclareol to the main product of sclareol glycol, which is the precursor of ambroxide. To date, knowledge is lacking about the effects of sclareol on cells and the proteins involved in sclareol metabolism. Comparative proteomic analyses were conducted on the strain H. roseonigra ATCC 20624 by using sclareol or glucose as the sole carbon source. A total of 79 up-regulated protein spots with a >2...
April 24, 2018: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29773073/metabolome-analysis-based-design-and-engineering-of-a-metabolic-pathway-in-corynebacterium-glutamicum-to-match-rates-of-simultaneous-utilization-of-d-glucose-and-l-arabinose
#14
Hideo Kawaguchi, Kumiko Yoshihara, Kiyotaka Y Hara, Tomohisa Hasunuma, Chiaki Ogino, Akihiko Kondo
BACKGROUND: L-Arabinose is the second most abundant component of hemicellulose in lignocellulosic biomass, next to D-xylose. However, few microorganisms are capable of utilizing pentoses, and catabolic genes and operons enabling bacterial utilization of pentoses are typically subject to carbon catabolite repression by more-preferred carbon sources, such as D-glucose, leading to a preferential utilization of D-glucose over pentoses. In order to simultaneously utilize both D-glucose and L-arabinose at the same rate, a modified metabolic pathway was rationally designed based on metabolome analysis...
May 17, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29773063/conversion-of-protein-active-regions-into-peptidomimetic-therapeutic-leads-using-backbone-cyclization-and-cycloscan-how-to-do-it-yourself
#15
Samuel J S Rubin, Yftah Tal-Gan, Chaim Gilon, Nir Qvit
Protein-protein interactions (PPIs) are particularly important for controlling both physiologic and pathologic biological processes but are difficult to target due to their large and/or shallow interaction surfaces unsuitable for small molecules. Linear peptides found in nature interact with some PPIs, and protein active regions can be used to design synthetic peptide compounds for inhibition of PPIs. However, linear peptides are limited therapeutically by poor metabolic and conformational stability, which can compromise their bioactivity and half-life...
May 17, 2018: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29772713/genetic-optimization-algorithm-for-metabolic-engineering-revisited
#16
Tobias B Alter, Lars M Blank, Birgitta E Ebert
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research...
May 16, 2018: Metabolites
https://www.readbyqxmd.com/read/29772009/ptra-a-reporter-system-for-monitoring-the-intracellular-dynamics-of-gene-expression
#17
Sabine G Wagner, Martin Ziegler, Hannes Löwe, Andreas Kremling, Katharina Pflüger-Grau
The presence of standardised tools and methods to measure and represent accurately biological parts and functions is a prerequisite for successful metabolic engineering and crucial to understand and predict the behaviour of synthetic genetic circuits. Many synthetic gene networks are based on transcriptional circuits, thus information on transcriptional and translational activity is important for understanding and fine-tuning the synthetic function. To this end, we have developed a toolkit to analyse systematically the transcriptional and translational activity of a specific synthetic part in vivo...
2018: PloS One
https://www.readbyqxmd.com/read/29770981/a-dehydrogenase-dual-hydrogen-abstraction-mechanism-promotes-estrogen-biosynthesis-can-we-expand-the-functional-annotation-of-the-aromatase-enzyme
#18
Angelo Spinello, Matic Pavlin, Lorenzo Casalino, Alessandra Magistrato
Cytochromes P450 (CYP450) are involved in the metabolism of exogenous compounds and in the synthesis of signaling molecules. Among the latter, human aromatase (HA) promotes estrogen biosynthesis, being a key pharmacological target against breast cancers. After decades of debate, the interest in gaining a comprehensive picture of HA catalysis has been renewed by the recent discovery that Compound I (Cpd I) is the reactive species of the peculiar aromatization step. Here, we provide for the first time a complete atomic-level picture of all controversial steps of estrogen biosynthesis...
May 17, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29770379/the-limits-to-biocatalysis-pushing-the-envelope
#19
Roger A Sheldon, Dean Brady
In the period 1985 to 1995 applications of biocatalysis, driven by the need for more sustainable manufacture of chemicals and catalytic, (enantio)selective methods for the synthesis of pharmaceutical intermediates, largely involved the available hydrolases. This was followed, in the next two decades, by revolutionary developments in protein engineering and directed evolution for the optimisation of enzyme function and performance that totally changed the biocatalysis landscape. In the same period, metabolic engineering and synthetic biology revolutionised the use of whole cell biocatalysis in the synthesis of commodity chemicals by fermentation...
May 17, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29769672/pancreas-regeneration
#20
REVIEW
Qiao Zhou, Douglas A Melton
The pancreas is made from two distinct components: the exocrine pancreas, a reservoir of digestive enzymes, and the endocrine islets, the source of the vital metabolic hormone insulin. Human islets possess limited regenerative ability; loss of islet β-cells in diseases such as type 1 diabetes requires therapeutic intervention. The leading strategy for restoration of β-cell mass is through the generation and transplantation of new β-cells derived from human pluripotent stem cells. Other approaches include stimulating endogenous β-cell proliferation, reprogramming non-β-cells to β-like cells, and harvesting islets from genetically engineered animals...
May 2018: Nature
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