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https://www.readbyqxmd.com/read/27933456/penicillin-v-acylases-from-gram-negative-bacteria-degrade-n-acylhomoserine-lactones-and-attenuate-virulence-in-pseudomonas-aeruginosa
#1
Avinash Vellore Sunder, Putri Dwi Utari, Sureshkumar Ramasamy, Ronald van Merkerk, Wim Quax, Archana Pundle
Virulence pathways in gram-negative pathogenic bacteria are regulated by quorum sensing mechanisms, through the production and sensing of N-acylhomoserine lactone (AHL) signal molecules. Enzymatic degradation of AHLs leading to attenuation of virulence (quorum quenching) could pave the way for the development of new antibacterials. Penicillin V acylases (PVAs) belong to the Ntn hydrolase superfamily, together with AHL acylases. PVAs are exploited widely in the pharmaceutical industry, but their role in the natural physiology of their native microbes is not clearly understood...
December 8, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27933454/improved-production-of-adipate-with-escherichia-coli-by-reversal-of-%C3%AE-oxidation
#2
Nicolai Kallscheuer, Jochem Gätgens, Marvin Lübcke, Jörg Pietruszka, Michael Bott, Tino Polen
The linear C6 dicarboxylic acid adipic acid is an important bulk chemical in the petrochemical industry as precursor of the polymer nylon-6,6-polyamide. In recent years, efforts were made towards the biotechnological production of adipate from renewable carbon sources using microbial cells. One strategy is to produce adipate via a reversed β-oxidation pathway. Hitherto, the adipate titers were very low due to limiting enzyme activities for this pathway. In most cases, the CoA intermediates are non-natural substrates for the tested enzymes and were therefore barely converted...
December 8, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27932460/protein-o-linked-mannose-%C3%AE-1-4-n-acetylglucosaminyltransferase-2-pomgnt2-is-a-gatekeeper-enzyme-for-functional-glycosylation-of-%C3%AE-dystroglycan
#3
Stephanie M Halmo, Danish Singh, Sneha Patel, Shuo Wang, Melanie Edlin, Geert-Jan Boons, Kelley W Moremen, David Live, Lance Wells
Disruption of the O-mannosylation pathway involved in functional glycosylation of α-dystroglycan gives rise to congenital muscular dystrophies. Protein O-linked mannose β-1,4-N-acetylglucosaminyltransferase 2 (POMGNT2) catalyzes the first step towards the functional matriglycan structure on α-dystroglycan that is responsible for binding extracellular matrix proteins and certain arenaviruses. Alternatively, protein O-linked mannose β-1,2-N-acetylglucosaminyltransferase 1 (POMGNT1) catalyzes the first step towards other various glycan structures present on α-dystroglycan of unknown function...
December 8, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27932313/3rd-congress-on-applied-synthetic-biology-in-europe-costa%C3%A2-da-caparica-portugal-february-2016
#4
Miguel Cueva
The third meeting organised by the European Federation of Biotechnology (EFB) on advances in Applied Synthetic Biotechnology in Europe (ASBE) was held in Costa da Caparica, Portugal, in February 2016. Abundant novel applications in synthetic biology were described in the six sessions of the meeting, which was divided into technology and tools for synthetic biology (I, II and III), bionanoscience, biosynthetic pathways and enzyme synthetic biology, and metabolic engineering and chemical manufacturing. The meeting presented numerous methods for the development of novel synthetic strains, synthetic biological tools and synthetic biology applications...
December 5, 2016: New Biotechnology
https://www.readbyqxmd.com/read/27930689/determination-of-a-screening-metric-for-high-diversity-dna-libraries
#5
Nicholas J Guido, Steven Handerson, Elaine M Joseph, Devin Leake, Li A Kung
The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants...
2016: PloS One
https://www.readbyqxmd.com/read/27930305/artemisia-annua-mutant-impaired-in-artemisinin-synthesis-demonstrates-importance-of-nonenzymatic-conversion-in-terpenoid-metabolism
#6
Tomasz Czechowski, Tony R Larson, Theresa M Catania, David Harvey, Geoffrey D Brown, Ian A Graham
Artemisinin, a sesquiterpene lactone produced by Artemisia annua glandular secretory trichomes, is the active ingredient in the most effective treatment for malaria currently available. We identified a mutation that disrupts the amorpha-4,11-diene C-12 oxidase (CYP71AV1) enzyme, responsible for a series of oxidation reactions in the artemisinin biosynthetic pathway. Detailed metabolic studies of cyp71av1-1 revealed that the consequence of blocking the artemisinin biosynthetic pathway is the redirection of sesquiterpene metabolism to a sesquiterpene epoxide, which we designate arteannuin X...
December 7, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27928941/molecular-dynamics-analysis-of-the-structural-and-dynamic-properties-of-the-functionally-enhanced-hepta-variant-of-mouse-5-aminolevulinate-synthase
#7
Insung Na, Shelly DeForte, Bosko M Stojanovski, Gloria C Ferreira, Vladimir N Uversky
Heme biosynthesis, a complex, multistage, and tightly controlled process, starts with 5-aminolevulinate (ALA) production, which, in metazoa and certain bacteria, is a reaction catalyzed by 5-aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. Functional aberrations in ALAS are associated with several human diseases. ALAS can adopt open and closed conformations, with segmental rearrangements of a C-terminal, 16-amino acid loop and an α-helix regulating accessibility to the ALAS active site...
December 8, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27925592/enzyme-free-scalable-dna-digital-design-techniques-a-review
#8
Aby Konampurath George, Harpreet Singh
With the recent developments in DNA nanotechnology, DNA has been used as the basic building block for the design of nanostructures, autonomous molecular motors, various devices, and circuits. DNA is considered as a possible candidate for replacing silicon for designing digital circuits in a near future, especially in implantable medical devices, because of its parallelism, computational powers, small size, light weight, and compatibility with bio-signals. The research in DNA digital design is in early stages of development, and electrical and computer engineers are not much attracted towards this field...
December 2, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27924934/one-pot-synthesis-of-class-ii-lanthipeptide-bovicin-hj50-via-an-engineered-lanthipeptide-synthetase
#9
Jian Wang, Xiaoxuan Ge, Li Zhang, Kunling Teng, Jin Zhong
Lanthipeptides are a large class of bacteria-produced, ribosomally-synthesized and post-translationally modified peptides. They are recognized as peptide antibiotics because most of them exhibit potent antimicrobial activities against Gram-positive bacteria especially those that are phylogenetically related to producers. Maturation of class II lanthipeptide like bovicin HJ50 undergoes precursor modification by LanM and a subsequent leader peptide cleavage by LanT. Herein, via co-expression of precursor gene bovA, modification gene bovM and transporter gene bovT in Escherichia coli C43 (DE3), bioactive bovicin HJ50 was successfully produced and secreted...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924926/identification-of-protein-structural-elements-responsible-for-the-diversity-of-sequence-preferences-among-mini-iii-rnases
#10
Dawid Głów, Małgorzata Kurkowska, Justyna Czarnecka, Krzysztof Szczepaniak, Dariusz Pianka, Verena Kappert, Janusz M Bujnicki, Krzysztof J Skowronek
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924150/increasing-n-butanol-production-with-saccharomyces-cerevisiae-by-optimizing-acetyl-coa-synthesis-nadh-levels-and-trans-2-enoyl-coa-reductase-expression
#11
Virginia Schadeweg, Eckhard Boles
BACKGROUND: n-Butanol can serve as an excellent gasoline substitute. Naturally, it is produced by some Clostridia species which, however, exhibit only limited suitability for industrial n-butanol production. The yeast Saccharomyces cerevisiae would be an ideal host due to its high robustness in fermentation processes. Nevertheless, n-butanol yields and titers obtained so far with genetically engineered yeast strains are only low. RESULTS: In our recent work, we showed that n-butanol production via a clostridial acetoacetyl-CoA-derived pathway in engineered yeast was limited by the availability of coenzyme A (CoA) and cytosolic acetyl-CoA...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27924025/brenda-in-2017-new-perspectives-and-new-tools-in-brenda
#12
Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg
The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence. The information is manually extracted from primary literature and extended by text mining procedures, integration of external data and prediction algorithms. Approximately 3 million data from 83 000 enzymes and 137 000 literature references constitute the manually annotated core. Text mining procedures extend these data with information on occurrence, enzyme-disease relationships and kinetic data...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923567/an-experimental-modeling-of-trinomial-bioengineering-crp-rdna-and-transporter-engineering-within-single-cell-factory-for-maximizing-two-phase-bioreduction
#13
Souvik Basak, Sumanta Kumar Ghosh, Vinay Deep Punetha, Ashish N Aphale, Prabir K Patra, Nanda Gopal Sahoo
A carbonyl reductase (cr) gene from Candida glabrata CBS138 has been heterologously expressed in cofactor regenerating E. coli host to convert Ethyl-4-chloro-3-oxobutanoate (COBE) into Ethyl-4-chloro-3-hydroxybutanoate (CHBE). The CR enzyme exhibited marked velocity at substrate concentration as high as 363mM with highest turnover number (112.77±3.95s(-1)). Solitary recombineering of such catalytic cell reproduced CHBE 161.04g/L per g of dry cell weight (DCW). Introduction of combinatorially engineered crp (crp*, F136I) into this heterologous E...
December 3, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27920668/getting-mirna-therapeutics-into-the-target-cells-for-neurodegenerative-diseases-a-mini-review
#14
REVIEW
Ming Ming Wen
miRNAs play important roles in modulating gene expression in varying cellular processes and disease pathogenesis, including neurodegenerative diseases. Several miRNAs are expressed in the brain, control brain development and are identified as important biomarkers in the pathogenesis of motor-and neuro-cognitive diseases such as Alzheimer's (AD), Huntington's and Parkinson's diseases (PD) and amyotrophic lateral sclerosis. These remarkable miRNAs could be used as diagnostic markers and therapeutic targeting potential for many stressful and untreatable progressive neurodegenerative diseases...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27919839/heparin-hyaluronic-acid-hydrogel-for-efficient-cellular-activities-of-3d-encapsulated-adipose-derived-stem-cells
#15
Kihak Gwon, Eunsol Kim, Giyoong Tae
We have developed stem cell-responsive, heparin-hyaluronic acid (Hep-HA) hydrogel, crosslinked by thiolated heparin (Hep-SH) and methacrylated hyaluronic acid (HA-MA) via visible light mediated, thiol-ene reaction. Physical properties of the hydrogel (gelation time, storage modulus, and swelling ratio) were tunable by adjusting light intensity, initiator/polymer concentration, and precursor pH. Culture of human adipose derived mesenchymal stem cells (ADSCs) using this hydrogel was characterized and compared with the control hydrogels including Hep-PEG hydrogel, PEG-HA hydrogel...
December 2, 2016: Acta Biomaterialia
https://www.readbyqxmd.com/read/27919692/improved-production-of-2-fucosyllactose-in-engineered-escherichia-coli-by-expressing-putative-%C3%AE-1-2-fucosyltransferase-wcfb-from-bacteroides-fragilis
#16
Young-Wook Chin, Ji-Yeong Kim, Jae-Han Kim, Sang-Min Jung, Jin-Ho Seo
2'-Fucosyllactose (2-FL) is one of most abundant oligosaccharides in human milk, which is involved in many biological functions for infant health. Since 2-FL has a great potential in application to functional food materials and pharmaceuticals, several microbial systems for mass production of 2-FL have been developed in recent years. Microbial production of 2-FL was suggested to be influenced by a number of factors including fucosylation activity of α-1,2-fucosyltransferase. In the present study, the wcfB gene coding for α-1,2-fucosyltransferase from Bacteroides fragilis was screened from eleven candidates of putative α-1,2-fucosyltransferase...
December 2, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27918487/integrating-deoxyribozymes-into-colorimetric-sensing-platforms
#17
REVIEW
Dingran Chang, Sandy Zakaria, Mimi Deng, Nicholas Allen, Kha Tram, Yingfu Li
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection...
December 3, 2016: Sensors
https://www.readbyqxmd.com/read/27917951/catalytic-conversion-of-lipophilic-substrates-by-phase-constrained-enzymes-in-the-aqueous-or-in-the-membrane-phase
#18
Marcus Cebula, Ilke Simsek Turan, Birgitta Sjödin, Madhuranayaki Thulasingam, Joseph Brock, Volodymyr Chmyrov, Jerker Widengren, Hiroshi Abe, Bengt Mannervik, Jesper Z Haeggström, Agnes Rinaldo-Matthis, Engin U Akkaya, Ralf Morgenstern
Both soluble and membrane-bound enzymes can catalyze the conversion of lipophilic substrates. The precise substrate access path, with regard to phase, has however, until now relied on conjecture from enzyme structural data only (certainly giving credible and valuable hypotheses). Alternative methods have been missing. To obtain the first experimental evidence directly determining the access paths (of lipophilic substrates) to phase constrained enzymes we here describe the application of a BODIPY-derived substrate (PS1)...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917399/retinoids-and-retinal-diseases
#19
Philip D Kiser, Krzysztof Palczewski
Recent progress in molecular understanding of the retinoid cycle in mammalian retina stems from painstaking biochemical reconstitution studies supported by natural or engineered animal models with known genetic lesions and studies of humans with specific genetic blinding diseases. Structural and membrane biology have been used to detect critical retinal enzymes and proteins and their substrates and ligands, placing them in a cellular context. These studies have been supplemented by analytical chemistry methods that have identified small molecules by their spectral characteristics, often in conjunction with the evaluation of models of animal retinal disease...
October 2016: Annual Review of Vision Science
https://www.readbyqxmd.com/read/27917379/current-understanding-of-the-correlation-of-lignin-structure-with-biomass-recalcitrance
#20
REVIEW
Mi Li, Yunqiao Pu, Arthur J Ragauskas
Lignin, a complex aromatic polymer in terrestrial plants, contributes significantly to biomass recalcitrance to microbial and/or enzymatic deconstruction. To reduce biomass recalcitrance, substantial endeavors have been exerted on pretreatment and lignin engineering in the past few decades. Lignin removal and/or alteration of lignin structure have been shown to result in reduced biomass recalcitrance with improved cell wall digestibility. While high lignin content is usually a barrier to a cost-efficient application of bioresources to biofuels, the direct correlation of lignin structure and its concomitant properties with biomass remains unclear due to the complexity of cell wall and lignin structure...
2016: Frontiers in Chemistry
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