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https://www.readbyqxmd.com/read/29150512/a-genetic-system-for-the-thermophilic-acetogenic-bacterium-thermoanaerobacter-kivui
#1
Mirko Basen, Irina Geiger, Laura Henke, Volker Müller
Thermoanaerobacter kivui is one of the very few thermophilic acetogenic microorganisms. It grows optimally at 66°C on sugars but also lithotrophically with H2 + CO2 or with CO, producing acetate as major product. While a genome-derived model of acetogenesis has been developed, only few physiological or biochemical experiments towards the function of important enzymes in carbon and energy metabolism have been carried out. To address this issue, we developed a method for targeted, markerless gene deletions and for integration of genes into the genome of T...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150511/sulfolobus-acidocaldarius-uptakes-pentoses-via-a-cut2-type-abc-transporter-and-metabolizes-them-through-the-aldolase-independent-weimberg-pathway
#2
Michaela Wagner, Lu Shen, Andreas Albersmeier, Nienke van der Kolk, Sujin Kim, Jaeho Cha, Christopher Bräsen, Jörn Kalinowski, Bettina Siebers, Sonja-Verena Albers
Sulfolobus spp. possess a great metabolic versatility and grow heterotrophically on various carbon sources such as different sugars and peptides. Known sugar transporters in Archaea predominantly belong to ABC transport systems. Although several ABC transporters for sugar uptake have been characterized in the crenarchaeon Sulfolobus solfataricus, only one homologue of these transporters, the maltose/maltooligomer transporter, could be identified in the closely related Sulfolobus acidocaldarius Comparison of the transcriptome of S...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150499/understanding-functional-roles-of-native-pentose-specific-transporters-for-activating-dormant-pentose-metabolism-in-yarrowia-lipolytica
#3
Seunghyun Ryu, Cong T Trinh
Pentoses including xylose and arabinose are the second-most prevalent sugars of lignocellulosic biomass that can be harnessed for biological conversion. Although Yarrowia lipolytica has emerged as a promising industrial microorganism for production of high-value chemicals and biofuels, its native pentose metabolism is poorly understood. Our previous study demonstrated that Y. lipolytica (ATCC MYA-2613) has endogenous enzymes for D-xylose assimilation, but inefficient xylitol dehydrogenase causes Y. lipolytica to assimilate xylose poorly...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149798/reconstructing-biosynthetic-pathway-of-the-plant-derived-cancer-chemopreventive-precursor-glucoraphanin-in-escherichia-coli
#4
Han Yang, Feixia Liu, Yin Li, Bo Yu
Epidemiological data confirmed a strong correlation between regular consumption of cruciferous vegetables and lower cancer risk. This cancer preventive property is mainly attributed to the glucosinolate products, such as glucoraphanin found in broccoli that is derived from methionine. Here we report the first successful reconstruction of the complete biosynthetic pathway of glucoraphanin from methionine in Escherichia coli via gene selection, pathway design, and protein engineering. We used branched-chain amino transferase 3 to catalyze two transamination steps to ensure the purity of precursor molecules and used cysteine as a sulfur donor to simplify the synthesis pathway...
November 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29149288/overexpression-of-seipin1-increases-oil-in-hydroxy-fatty-acid-accumulating-seeds
#5
Daniel Lunn, James G Wallis, John Browse
While plant oils are an important source of food, plants also produce oils containing specialized fatty acids with chemical and physical properties valued in industry. Ricinoleic acid, a hydroxy-fatty acid (HFA) produced in the seed of castor (Ricinus communis), is of particular value with a wide range of applications. Since castor cultivation is currently successful only in tropic climates, and because castor seed contain the toxin ricin, there are ongoing efforts to develop a temperate crop capable of HFA biosynthesis...
November 15, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29147710/step-by-step-build-up-of-covalent-poly-ethylene-oxide-nanogel-films
#6
S Zahouani, L Hurman, M De Giorgi, C Vigier-Carrière, F Boulmedais, B Senger, B Frisch, P Schaaf, P Lavalle, L Jierry
Hydrogels based on poly(ethylene glycol) (PEG) are commonly used for studies related to cell fate and tissue engineering. Here we present a new covalent layer-by-layer build-up process leading to PEG coatings of nanometer size called "nanogel films". Compared to macroscopic hydrogels, such nanogels should provide a fine control over the structure and the thickness of the coating. Alternated deposition of bifunctional and tetra functional PEG molecules reacting through thiol/maleimide click chemistry is evaluated by quartz crystal microbalance...
November 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/29146470/combination-of-type-ii-fatty-acid-biosynthesis-enzymes-and-thiolases-supports-a-functional-%C3%AE-oxidation-reversal
#7
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/29144959/induction-of-innervation-by-encapsulated-adipocytes-with-engineered-vitamin-a-metabolism
#8
Q Shen, R Yasmeen, J Marbourg, L Xu, J L Yu, P Fadda, A Flechtner, L J Lee, P G Popovich, O Ziouzenkova
Innervation is a fundamental basis for function and survival of tissues. In the peripheral tissues, degenerative diseases create a neurotoxic metabolic milieu that either causes neurodegeneration or fails to sustain regenerative growth and reinnervation of injured/diseased tissues. Encapsulation of cells producing neurotrophic factors can augment axon growth and neuron survival; however, sustained innervation in vivo requires a combination of factors promoting axon growth and guidance pathway that are released in a tissue-specific context...
October 28, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/29142825/creating-metabolic-demand-as-an-engineering-strategy-in-pseudomonas-putida-rhamnolipid-synthesis-as-an-example
#9
Till Tiso, Petra Sabelhaus, Beate Behrens, Andreas Wittgens, Frank Rosenau, Heiko Hayen, Lars Mathias Blank
Metabolic engineering of microbial cell factories for the production of heterologous secondary metabolites implicitly relies on the intensification of intracellular flux directed toward the product of choice. Apart from reactions following peripheral pathways, enzymes of the central carbon metabolism are usually targeted for the enhancement of precursor supply. In Pseudomonas putida, a Gram-negative soil bacterium, central carbon metabolism, i.e., the reactions required for the synthesis of all 12 biomass precursors, was shown to be regulated at the metabolic level and not at the transcriptional level...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29142824/system-wide-cofactor-turnovers-can-propagate-metabolic-stability-between-pathways
#10
Y Yang, Y H Guan, J Villadsen
Metabolic homeostasis, or low-level metabolic steady state, has long been taken for granted in metabolic engineering, and research priority has always been given to understand metabolic flux control and regulation of the reaction network. In the past, this has not caused concerns because the metabolic networks studied were invariably associated with living cells. Nowadays, there are needs to reconstruct metabolic networks, and so metabolic homeostasis cannot be taken for granted. For metabolic steady state, enzyme feedback control has been known to explain why metabolites in metabolic pathways can avoid accumulation...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29142820/excessive-by-product-formation-a-key-contributor-to-low-isobutanol-yields-of-engineered-saccharomyces-cerevisiae-strains
#11
N Milne, S A Wahl, A J A van Maris, J T Pronk, J M Daran
It is theoretically possible to engineer Saccharomyces cerevisiae strains in which isobutanol is the predominant catabolic product and high-yielding isobutanol-producing strains are already reported by industry. Conversely, isobutanol yields of engineered S. cerevisiae strains reported in the scientific literature typically remain far below 10% of the theoretical maximum. This study explores possible reasons for these suboptimal yields by a mass-balancing approach. A cytosolically located, cofactor-balanced isobutanol pathway, consisting of a mosaic of bacterial enzymes whose in vivo functionality was confirmed by complementation of null mutations in branched-chain amino acid metabolism, was expressed in S...
December 2016: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29141885/a-role-for-bacterial-urease-in-gut-dysbiosis-and-crohn-s-disease
#12
Josephine Ni, Ting-Chin David Shen, Eric Z Chen, Kyle Bittinger, Aubrey Bailey, Manuela Roggiani, Alexandra Sirota-Madi, Elliot S Friedman, Lillian Chau, Andrew Lin, Ilana Nissim, Justin Scott, Abigail Lauder, Christopher Hoffmann, Gloriany Rivas, Lindsey Albenberg, Robert N Baldassano, Jonathan Braun, Ramnik J Xavier, Clary B Clish, Marc Yudkoff, Hongzhe Li, Mark Goulian, Frederic D Bushman, James D Lewis, Gary D Wu
Gut dysbiosis during inflammatory bowel disease involves alterations in the gut microbiota associated with inflammation of the host gut. We used a combination of shotgun metagenomic sequencing and metabolomics to analyze fecal samples from pediatric patients with Crohn's disease and found an association between disease severity, gut dysbiosis, and bacterial production of free amino acids. Nitrogen flux studies using (15)N in mice showed that activity of bacterial urease, an enzyme that releases ammonia by hydrolysis of host urea, led to the transfer of murine host-derived nitrogen to the gut microbiota where it was used for amino acid synthesis...
November 15, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/29141528/engineering-clostridium-absonum-7%C3%AE-hydroxysteroid-dehydrogenase-for-enhancing-thermostability-based-on-flexible-site-and-%C3%AE-%C3%AE-g-prediction
#13
Deshuai Lou, Jun Tan, Liancai Zhu, Shunlin Ji, Shijin Tang, Kaiyi Yao, Jingxuan Han, Bochu Wang
Enhancing thermostability of the 7α-Hydroxysteroid dehydrogenases (7α-HSDHs) is beneficial to its industrial application broadly. Based on unfolding free energy changes (ΔΔG) prediction seven mutations of Clostridium absonum (CA) 7α-HSDH were selected and experimentally verified, and these mutants fitted three-state denaturation model well, among which S22L located in the αA possessed the greatest TmN→I increase (>8 °C). Mutants P124L, L197E, N171L and Y259E also became more stable than wild type CA 7α-HSDH with different ranges...
November 12, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29140084/characterization-of-a-ugt84-family-glycosyltransferase-provides-new-insights-into-substrate-binding-and-reactivity-of-galloylglucose-ester-forming-ugts
#14
Alexander E Wilson, Xiaoxue Feng, Nadia N Ono, Doron Holland, Rachel Amir, Li Tian
Galloylated plant specialized metabolites play important roles in plant-environment interactions as well as the promotion of human and animal health. The galloylation reactions are mediated by the formation of galloylglucose esters from gallic acid and UDP-glucose, catalyzed by the plant UGT84 family glycosyltransferases. To explore and exploit the structural determinants of UGT84 activities, we performed homology modeling and substrate docking of PgUGT84A23, a galloylglucose ester-forming family 84 UGT, as well as sequence comparisons of PgUGT84A23 with other functionally characterized plant UGTs...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29138389/phage-display-and-selection-of-lanthipeptides-on-the-carboxy-terminus-of-the-gene-3-minor-coat-protein
#15
Johannes H Urban, Markus A Moosmeier, Tobias Aumüller, Marcus Thein, Tjibbe Bosma, Rick Rink, Katharina Groth, Moritz Zulley, Katja Siegers, Kathrin Tissot, Gert N Moll, Josef Prassler
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an emerging class of natural products with drug-like properties. To fully exploit the potential of RiPPs as peptide drug candidates, tools for their systematic engineering are required. Here we report the engineering of lanthipeptides, a subclass of RiPPs characterized by multiple thioether cycles that are enzymatically introduced in a regio- and stereospecific manner, by phage display. This was achieved by heterologous co-expression of linear lanthipeptide precursors fused to the widely neglected C-terminus of the bacteriophage M13 minor coat protein pIII, rather than the conventionally used N-terminus, along with the modifying enzymes from distantly related bacteria...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29138095/kinetics-and-thermodynamics-of-the-thermal-inactivation-and-chaperone-assisted-folding-of-zebrafish-dihydrofolate-reductase
#16
Charu Thapliyal, Neha Jain, Naira Rashid, Pratima Chaudhuri
The maintenance of thermal stability is a major issue in protein engineering as many proteins tend to form inactive aggregates at higher temperatures. Zebrafish DHFR, an essential protein for the survival of cells, shows irreversible thermal unfolding transition. The protein exhibits complete unfolding and loss of activity at 50 °C as monitored by UV-Visible, fluorescence and far UV-CD spectroscopy. The heat induced inactivation of zDHFR follows first-order kinetics and Arrhenius law. The variation in the value of inactivation rate constant, k with increasing temperatures depicts faster inactivation at elevated temperatures...
November 11, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29134460/enzyme-based-electrobiotechnological-synthesis
#17
Lisa Marie Schmitz, Katrin Rosenthal, Stephan Lütz
Oxidoreductases are enzymes with a high potential for organic synthesis, as their selectivity often exceeds comparable chemical syntheses. The biochemical cofactors of these enzymes need regeneration during synthesis. Several regeneration methods are available but the electrochemical approach offers an efficient and quasi mass-free method for providing the required redox equivalents. Electron transfer systems involving direct regeneration of natural and artificial cofactors, indirect electrochemical regeneration via a mediator, and indirect electroenzymatic cofactor regeneration via enzyme and mediator have been investigated...
November 14, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29133410/unprecedented-pathway-of-reducing-equivalents-in-a-diflavin-linked-disulfide-oxidoreductase
#18
Rubén M Buey, Juan B Arellano, Luis López-Maury, Sergio Galindo-Trigo, Adrián Velázquez-Campoy, José L Revuelta, José M de Pereda, Francisco J Florencio, Peter Schürmann, Bob B Buchanan, Monica Balsera
Flavoproteins participate in a wide variety of physiologically relevant processes that typically involve redox reactions. Within this protein superfamily, there exists a group that is able to transfer reducing equivalents from FAD to a redox-active disulfide bridge, which further reduces disulfide bridges in target proteins to regulate their structure and function. We have identified a previously undescribed type of flavin enzyme that is exclusive to oxygenic photosynthetic prokaryotes and that is based on the primary sequence that had been assigned as an NADPH-dependent thioredoxin reductase (NTR)...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29133008/biotechnological-potential-of-novel-glycoside-hydrolase-family-70-enzymes-synthesizing-%C3%AE-glucans-from-starch-and-sucrose
#19
REVIEW
Joana Gangoiti, Tjaard Pijning, Lubbert Dijkhuizen
Transglucosidases belonging to the glycoside hydrolase (GH) family 70 are promising enzymatic tools for the synthesis of α-glucans with defined structures from renewable sucrose and starch substrates. Depending on the GH70 enzyme specificity, α-glucans with different structures and physicochemical properties are produced, which have found diverse (potential) commercial applications, e.g. in food, health and as biomaterials. Originally, the GH70 family was established only for glucansucrase enzymes of lactic acid bacteria that catalyze the synthesis of α-glucan polymers from sucrose...
November 10, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/29131622/computational-study-of-engineered-cytochrome-p450-catalyzed-c-h-amination-the-origin-of-the-regio-and-stereoselectivity
#20
Zhe Li, D Jean Burnell, Russell Jaye Boyd
Cytochrome P450 enzymes were recently engineered to catalyze the C-H amination reaction of aryl sulfonyl azides with excellent regio- and stereoselectivity (Arnold and coworkers JACS, 2014, 136, 15505). The mechanism of this reaction was studied by quantum mechanical (QM)/molecular mechanical (MM) calculations in this work. The C-H activation is found to be a stepwise process consisting of hydrogen abstraction (H-abstraction) of the reactive C-H bond by an iron nitrenoid cofactor to produce the biradical intermediate and the subsequent radical rebinding to form the final product...
November 13, 2017: Journal of Physical Chemistry. B
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